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Plasmid- and strain-specific factors drive variation in ESBL-plasmid spread in vitro and in vivo
<p>Horizontal gene transfer, mediated by conjugative plasmids, is a major driver of the global rise of antibiotic resistance. However, the relative contributions of factors that underlie the spread of plasmids and their roles in conjugation in vivo are unclear. To address this, we investigated the spread of clinical Extended Spectrum Beta-Lactamase (ESBL)-producing plasmids in the absence of antibiotics in vitro and in the mouse intestine. We hypothesised that plasmid properties would be the primary determinants of plasmid spread and that bacterial strain identity would also contribute. We found clinical Escherichia coli strains natively associated with ESBL-plasmids conjugated to three distinct E. coli strains and one Salmonella enterica serovar Typhimurium strain. Final transconjugant frequencies varied across plasmid, donor, and recipient combinations, with qualitative consistency when comparing transfer in vitro and in vivo in mice. In both environments, transconjugant frequencies for these natural strains and plasmids covaried with the presence/absence of transfer genes on ESBL-plasmids and were affected by plasmid incompatibility. By moving ESBL-plasmids out of their native hosts, we showed that donor and recipient strains also modulated transconjugant frequencies. This suggests that plasmid spread in the complex gut environment of animals and humans can be predicted based on in vitro testing and genetic data.</p>
Data from: Chimpanzees behave prosocially in a group-specific manner
<p><span><span><span><span><span><span><span><span><span><span><span>Chimpanzees act cooperatively in the wild, but whether they afford benefits to others, and whether their tendency to act prosocially varies across communities is unclear. Here, we show that chimpanzees from neighboring communities provide valuable resources to group members at personal cost, and that the magnitude of their prosocial behavior is group specific. Provided with a resource-donation experiment allowing for free (partner) choice, we observed an increase in prosocial acts across the study period in the majority of chimpanzees. When group members could profit (test condition), chimpanzees provided resources more frequently and for longer durations than when their acts produced inaccessible resources (control condition). Strikingly, chimpanzees' prosocial behavior was group specific, with more socially tolerant groups acting more prosocially. We conclude that chimpanzees may purposely behave prosocially toward group members, and that the notion of group-specific sociality in nonhuman animals should crucially inform discussions on the evolution of prosocial behavior.</span></span></span></span></span></span></span></span></span></span></span></p>
Plumage and eggshell colouration covary with the level of sex-specific parental contributions to nest building in birds
<p>Interspecific variation in sex-specific contributions to prenatal parental care, including avian nest building, remain poorly understood. Here, we examined whether the colouration of the parents and of their eggs covary with sex-specific nest building contributions in 521 species of Western Palearctic birds. Having colourful plumages and laying colourful eggs are both costly because of the deposition of pigments (in feathers and eggs) and/or forming costly nanostructural substrates (in feathers), and so it is expected that those costs are traded-off against the costs of nest building. We therefore tested two predictions of this trade-off hypothesis, namely that species in which females alone build nests (1) exhibit sexual plumage dichromatism in that females are less colourful than males and (2) lay less colourful eggs. Using a phylogenetically-informed comparative approach, we found support for the first prediction so that species in which females build nests alone or together with males are more likely to be dichromatic in plumage. Meanwhile, regarding the second prediction, contrary to our expectation, we found that species in which females build nests alone or together with males are more likely to lay colourfully pigmented eggs relative to species in which only males build nests. This suggests that sex differences in plumage colouration and egg colouration covary in a complex manner with female pre-copulatory investment in reproduction at the interspecific level.</p>
On the Understandability of Language Constructs to Structure the State and Behavior in Abstract State Machine Specifications: A Controlled Experiment
<p>Data-Set and Artifacts: Documents, Forms, and R Scripts for Reproducibility of the Empirical Study</p>
Human RNA-specific Amplicons
<p>Primers to specifically amplify human cDNA (not genomic DNA) from the EDF1 and NEDD8 genes.</p>
Data from: Comparison of taxon-specific versus general locus sets for targeted sequence capture for plant phylogenomics
Premise of the study: Targeted sequence capture can be used to efficiently gather sequence data for large numbers of loci, such as single-copy nuclear loci. Most published studies in plants have used taxon-specific locus sets developed individually for a clade using multiple genomic and transcriptomic resources. General locus sets can also be developed from loci that have been identified as single-copy and having orthologs in large clades of plants. Methods: We identify and compare a taxon-specific locus set and three general locus sets (COSII, APVO SSC, PPR) for targeted sequence capture in Buddleja (Scrophulariaceae) and outgroups. We evaluate their performance in terms of assembly success, sequence variability, and resolution and support of inferred phylogenetic trees. Results: The taxon-specific locus set had the most target loci. Assembly success was high for all locus sets in Buddleja samples. For outgroups, general locus sets had greater assembly success. Taxon-specific and PPR loci had the highest average variability. The taxon-specific dataset produced the best supported tree, but all datasets showed improved resolution over previous non-sequence capture datasets. Discussion: General loci can be a useful source of sequence capture targets, especially if multiple genomic resources are not available for a taxon.
Data from: Life table invasion models: spatial progression and species-specific partitioning
Biological invasions are increasingly being considered important spatial processes that drive global changes, threatening biodiversity, regional economies, and ecosystem functions. A unifying conceptual model of the invasion dynamics could serve as a useful tool for comparison and classification of invasion processes involving different species across large geographic ranges. By dividing these geographic ranges that are subject to invasions into discrete spatial units we here conceptualize the invasion process as the transition from pristine to invaded spatial units. We use California cities as the spatial units and a long-term database of invasive tropical tephritids to characterize the invasion patterns. A new life-table method based on insect demography, including the progression model of invasion stage transition and the species-specific partitioning model of multispecies invasions, was developed to analyze the invasion patterns. The progression model allows us to estimate the probability and rate of transition, for individual cities, from pristine to infested stages and subsequently differentiate first year of detection from detection recurrences. Importantly, we show that the interval of invasive tephritid recurrence in a city declines with increasing invasion stages of the city. The species-specific partitioning model revealed profound difference in invasion outcome depending on which tephritid species was first detected (and then locally eradicated) in the early stage of invasion. Taken together, we discuss how these two life-table invasion models can cast new light on existing invasion concepts; in particular, on formulating invasion dynamics as the state transition of cities and partitioning species-specific role during multispecies invasions. These models provide a new set of tools for predicting the spatiotemporal progression of invasion and providing early warnings of recurrent invasions for efficient management.
Data from: How to fight multiple enemies: target-specific chemical defences in an aposematic moth
Animals have evolved different defensive strategies to survive predation, among which chemical defences are particularly widespread and diverse. Here we investigate the function of chemical defence diversity, hypothesising that such diversity has evolved as a response to multiple enemies. The aposematic wood tiger moth (Arctia plantaginis) displays conspicuous hindwing colouration and secretes two distinct defensive fluids, from their thoracic glands and abdomen. We presented fluids from lab-reared moths to two biologically relevant predators, birds and ants, and measured their reaction in controlled bioassays (no information on colour was provided). We found that defensive fluids are target-specific: thoracic fluids, and particularly the 2-sec-butyl-3-methoxypyrazine (SBMP) which they contain, deterred birds, but caused no aversive response in ants. In contrast, abdominal fluids were particularly deterrent to ants, while birds did not find them repellent. Our study is the first to show evidence of a single species producing separate chemical defences targeted to different predator types, highlighting the importance of taking into account complex predator communities in studies on the evolution of prey defence diversity.
Data from: Genetic analysis of the peatmoss Sphagnum cribrosum (Sphagnaceae) indicates independent origins of an extreme infra-specific morphology shift
Within Sphagnum cribrosum, a dioicous aquatic peatmoss, a unique morphological variant (the "waveform"), found at only two lakes in North Carolina, has a branching architecture that is extremely differentiated from anything otherwise known in Sphagnum, though the plants are microscopically indistinguishable from S. cribrosum. At one site where the two morphologies co-occur, sixty years of field observations demonstrate the persistence of each morphology, even where the two forms grow intermixed. We conducted a reciprocal transplant experiment in which waveform and normal plants maintained their divergent morphologies for eight months. We sampled populations throughout the range and conducted genetic and phylogenetic analyses with microsatellite markers and DNA sequences to investigate the genetic context of the waveform morphology within S. cribrosum. Haplotype networks from DNA sequences showed the two waveform populations are separated by 11 substitutions across three loci. Microsatellite analyses using non-parametric clustering and admixture models also indicated genetic dissimilarity between genotypes with waveform morphology at the two lakes. Both molecular datasets suggest that the waveform morphology had at least two independent origins despite proximity of the two lakes where it uniquely occurs. Given the clonal nature of the waveform, it is unlikely to form a cohesive evolutionary lineage deserving of taxonomic status. The analysis also revealed a genetically diverse population in Georgia as the potential source of variation found in all other populations of S. cribrosum.
Data from: Sex-specific patterns of aging on sexual ornaments and gametes
Sex differences in age-dependent mortality and reproductive success are predicted to drive the evolution of sexually dimorphic patterns of reproductive investment over life. However, this prediction has not been fully explored because it is difficult to measure primary and secondary sexual traits over the life spans of males and females. Here we studied a population of fowl, Gallus gallus, to gain longitudinal data on a sexual ornament (the comb), quantity of gametes produced, and gamete quality (sperm velocity and egg mass) of males and females. Our results reveal pronounced differences between the sexes in age-specific patterns of reproductive investment. In males, comb size decreased linearly with age, high sperm quality early in life was associated with reduced sperm quality late in life, and high sperm production was related to early death. In contrast, female comb size and egg mass were maximized at intermediate ages, and fecundity was independent of life span. Finally, the way traits were related in males did not change over life, whereas in females the association between fecundity and comb size changed from positive to negative over the lifetime of a female, indicating that aging may lead to trade-offs in investment between traits in females. These results show that males and females differ in reproductive investment with age, in terms of both the expression of individual traits and their phenotypic covariance.
Data from: Phylogenetic plant community structure along elevation is lineage specific
The trend of closely related taxa to retain similar environmental preferences mediated by inherited traits suggests that several patterns observed at the community scale originate from longer evolutionary processes. While the effects of phylogenetic relatedness have been previously studied within a single genus or family, lineage-specific effects on the ecological processes governing community assembly have rarely been studied for entire communities or flora. Here, we measured how community phylogenetic structure varies across a wide elevation gradient for plant lineages represented by 35 families, using a co-occurrence index and net relatedness index (NRI). We propose a framework that analyses each lineage separately and reveals the trend of ecological assembly at tree nodes. We found prevailing phylogenetic clustering for more ancient nodes and overdispersion in more recent tree nodes. Closely related species may thus rapidly evolve new environmental tolerances to radiate into distinct communities, while older lineages likely retain inherent environmental tolerances to occupy communities in similar environments, either through efficient dispersal mechanisms or the exclusion of older lineages with more divergent environmental tolerances. Our study illustrates the importance of disentangling the patterns of community assembly among lineages to better interpret the ecological role of traits. It also sheds light on studies reporting absence of phylogenetic signal, and opens new perspectives on the analysis of niche and trait conservatism across lineages.
Data from: Specific leaf area predicts dryland litter decomposition via two mechanisms
1. Litter decomposition plays important roles in carbon and nutrient cycling. In dryland both microbial decomposition and abiotic degradation (by UV light or other forces) drive variation in decomposition rates, but whether and how litter traits and position determine the balance between these processes is poorly understood. 2. We investigated relationships between litter quality and their decomposition rates among diverse plant species in a desert ecosystem in vertically contrasting positions representing distinct decomposition environments driven by different relative contributions of abiotic and microbial degradation. Thereto, leaf litter samples from 17 desert species were sealed into litterbags and placed on the soil surface under strong solar exposure versus shade conditions, or buried in the soil at 10 cm depth, for a whole year. 3. Litter decomposition rates were 21 and 17 % higher in burial and light-exposed treatments, respectively, than those in shade. Leaf traits, i.e. specific leaf area (SLA), litter C:N ratio and lignin concentration could predict litter decomposition to some degree, but their predictive power was dependent on litter position. However, multiple linear regression showed that SLA, litter C and P significantly affected k values for leaf litter decomposition besides litter position, with SLA standing out as a strong determinant of litter decomposition rate as related either to solar radiation or the environment below the soil surface. Furthermore, the interspecific differences in litter decomposition rate decreased over time, implying that afterlife effects of leaf traits on decomposition were attenuated. 4. Synthesis. These findings suggest that abiotic photodegradation and soil burial mediated microbial decomposition could be responsible for higher than expected litter turnover in dryland. They point to a dual role of specific leaf area as a promotor of decomposition rates: via relative exposure of the leaf surface to abiotic factors such as UV light versus to soil moisture and microbes under soil burial.
Data from: Variations in age- and sex-specific survival rates help explain population trend in a discrete marine mammal population
1. Understanding the drivers underlying fluctuations in the size of animal populations is central to ecology, conservation biology and wildlife management. Reliable estimates of survival probabilities are key to population viability assessments, and patterns of variation in survival can help inferring the causal factors behind detected changes in population size. 2. We investigated whether variation in age and sex-specific survival probabilities could help explain the increasing trend in population size detected in a small, discrete population of bottlenose dolphins Tursiops truncatus off the east coast of Scotland. 3. To estimate annual survival probabilities we applied capture-recapture models to photo-identification data collected from 1989 to 2015. We used robust design models accounting for temporary emigration to estimate juvenile and adult survival, multi-state models to estimate sex-specific survival, and age-models to estimate calf survival. 4. We found strong support for an increase in juvenile/adult annual survival from 93.1% to 96.0% over the study period, most likely caused by a change in juvenile survival. Examination of sex-specific variation showed weaker support for this trend being a result of increasing female survival, which was overall higher than for males and animals of unknown sex. Calf survival was lower in the first than second year; a bias in estimating third-year survival will likely exist in similar studies. There was some support first-born calf survival being lower than for calves born subsequently. 5. Coastal marine mammal populations are subject to the impacts of environmental change, increasing anthropogenic disturbance and the effects of management measures. Survival estimates are essential to improve our understanding of population dynamics and help predict how future pressures may impact populations, but obtaining robust information on the life history of long-lived species is challenging. Our study illustrates how knowledge of survival can be increased by applying a robust analytical framework to photo-identification data.
Data from: Nuclear introns outperform mitochondrial DNA in inter-specific phylogenetic reconstruction: Lessons from horseshoe bats (Rhinolophidae: Chiroptera)
Despite many studies illustrating the perils of utilising mitochondrial DNA in phylogenetic studies, it remains one of the most widely used genetic markers for this purpose. Over the last decade, nuclear introns have been proposed as alternative markers for phylogenetic reconstruction. However, the resolution capabilities of mtDNA and nuclear introns have rarely been quantified and compared. In the current study we generated a novel ∼5 kb dataset comprising six nuclear introns and a mtDNA fragment. We assessed the relative resolution capabilities of the six intronic fragments with respect to each other, when used in various combinations together, and when compared to the traditionally used mtDNA. We focused on a major clade in the horseshoe bat family (Afro-Palaearctic clade; Rhinolophidae) as our case study. This old, widely distributed and speciose group contains a high level of conserved morphology. This morphological stasis renders the reconstruction of the phylogeny of this group with traditional morphological characters complex. We sampled multiple individuals per species to represent their geographic distributions as best as possible (122 individuals, 24 species, 68 localities). We reconstructed the species phylogeny using several complementary methods (partitioned Maximum Likelihood and Bayesian and Bayesian multispecies-coalescent) and made inferences based on consensus across these methods. We computed pairwise comparisons based on Robinson–Foulds tree distance metric between all Bayesian topologies generated (27,000) for every gene(s) and visualised the tree space using multidimensional scaling (MDS) plots. Using our supported species phylogeny we estimated the ancestral state of key traits of interest within this group, e.g. echolocation peak frequency which has been implicated in speciation. Our results revealed many potential cryptic species within this group, even in taxa where this was not suspected a priori and also found evidence for mtDNA introgression. We demonstrated that by using just two introns one can recover a better supported species tree than when using the mtDNA alone, despite the shorter overall length of the combined introns. Additionally, when combining any single intron with mtDNA, we showed that the result is highly similar to the mtDNA gene tree and far from the true species tree and therefore this approach should be avoided. We caution against the indiscriminate use of mtDNA in phylogenetic studies and advocate for pilot studies to select nuclear introns. The selection of marker type and number is a crucial step that is best based on critical examination of preliminary or previously published data. Based on our findings and previous publications, we recommend the following markers to recover phylogenetic relationships between recently diverged taxa (<20 My) in bats and other mammals: ACOX2, COPS7A, BGN, ROGDI and STAT5A.
Data from: Host specificity shapes population structure of pinworm parasites in Caribbean reptiles
Host specificity is one of the potential factors affecting parasite diversification because gene flow may be facilitated or constrained by the number of host species that a parasite can exploit. We test this hypothesis using a costructure approach, comparing two sympatric pinworm parasites that differ in host specificity – Parapharyngodon cubensis and Spauligodon anolis – on the Puerto Rican Bank and St. Croix in the Caribbean. Spauligodon anolis specializes on Anolis lizards, whereas P. cubensis parasitizes Anolis lizards as well as many other species of lizards and snakes. We collected lizards from across the Puerto Rican Bank and St. Croix, sampled them for S. anolis and P. cubensis and generated nuclear and mitochondrial sequence data from the parasites. We used these data to show that P. cubensis is comprised of multiple cryptic species that exhibit limited population structure relative to S. anolis, which is consistent with our prediction based on their host specificity. We also provide evidence that the distribution of P. cubensis species is maintained by competitive exclusion, and in contrast to previous theoretical work, the parasites with the greatest number of host species also reach the highest prevalence rates. Overall, our results are consistent with the hypothesis that host specificity shapes parasite diversification, and suggest that even moderate differences in host specificity may contribute to substantial differences in diversification.
Data from: Hyaluronan and N-ERC/mesothelin as key biomarkers in a specific two-step model to predict pleural malignant mesothelioma
Purpose: Diagnosis of malignant mesothelioma is challenging. The first available diagnostic material is often an effusion and biochemical analysis of soluble markers may provide additional diagnostic information. This study aimed to establish a predictive model using biomarkers from pleural effusions, to allow early and accurate diagnosis. Patients and Methods: Effusions were collected prospectively from 190 consecutive patients at a regional referral centre. Hyaluronan, N-ERC/mesothelin, C-ERC/mesothelin, osteopontin, syndecan-1, syndecan-2, and thioredoxin were measured using ELISA and HPLC. A predictive model was generated and validated using a second prospective set of 375 effusions collected consecutively at a different referral centre. Results: Biochemical markers significantly associated with mesothelioma were hyaluronan (odds ratio, 95% CI: 8.82, 4.82–20.39), N-ERC/mesothelin (4.81, 3.19–7.93), CERC/mesothelin (3.58, 2.43–5.59) and syndecan-1 (1.34, 1.03–1.77). A two-step model using hyaluronan and N-ERC/mesothelin, and combining a threshold decision rule with logistic regression, yielded good discrimination with an area under the ROC curve of 0.99 (95% CI: 0.97–1.00) in the model generation dataset and 0.83 (0.74–0.91) in the validation dataset, respectively. Conclusions: A two-step model using hyaluronan and N-ERC/mesothelin predicts mesothelioma with high specificity. This method can be performed on the first available effusion and could be a useful adjunct to the morphological diagnosis of mesothelioma.
Data from: Sex-specific winter distribution in a sexually dimorphic shorebird is explained by resource partitioning
Sexual size dimorphism (SSD) implies correlated differences in energetic requirements and feeding opportunities, such that sexes will face different trade-offs in habitat selection. In seasonal migrants, this could result in a differential spatial distribution across the wintering range. To identify the ecological causes of sexual spatial segregation, we studied a sexually dimorphic shorebird, the bar-tailed godwit Limosa lapponica, in which females have a larger body and a longer bill than males. With respect to the trade-offs that these migratory shorebirds experience in their choice of wintering area, northern and colder wintering sites have the benefit of being closer to the Arctic breeding grounds. According to Bergmann's rule, the larger females should incur lower energetic costs per unit of body mass over males, helping them to winter in the cold. However, as the sexes have rather different bill lengths, differences in sex-specific wintering sites could also be due to the vertical distribution of their buried prey, that is, resource partitioning. Here, in a comparison between six main intertidal wintering areas across the entire winter range of the lapponica subspecies in northwest Europe, we show that the percentage of females between sites was not correlated with the cost of wintering, but was positively correlated with the biomass in the bottom layer and negatively with the biomass in the top layer. We conclude that resource partitioning, rather than relative expenditure advantages, best explains the differential spatial distribution of male and female bar-tailed godwits across northwest Europe.
Data from: Tropical dung beetle morphological traits predict functional traits and show intra-specific differences across land uses
1. Functional traits and functional diversity measures are increasingly being used to examine land use effects on biodiversity and community assembly rules. 2. Morphological traits are frequently derived from a mean value of many individuals, and used directly as functional traits. However, this approach overlooks the importance of intraspecific differences. 3. We collected morphometric data from over 1700 individuals of 12 species of dung beetle to establish whether morphological measurements can be used as predictors of behavioral traits. We also compared morphology among individuals collected from different land uses to identify if intra-specific differences in morphology vary among land use types. 4. We show that leg and eye measurements can be used to predict dung beetle nesting behavior and period of activity, and used this information to confirm the previously unresolved nesting behavior for Synapsis ritsemae. 5. We found intra-specific differences in morphological traits across different land use types. Phenotypic plasticity was found for traits associated with dispersal (wing aspect ratio and wing loading) and reproductive capacity (abdomen size). 6. The ability to predict behavioral functional traits from morphology is useful where the behavior of dung beetles cannot be directly observed, especially in tropical environments where the ecology of many species is poorly understood. 7. There have been very few studies investigating variability in animal traits. We provide evidence that land use change can cause phenotypic plasticity in tropical dung beetle species. Our results reinforce recent calls for intraspecific variation in traits to receive more attention within community ecology.
Data from: Season-specific and guild-specific effects of anthropogenic landscape modification on metacommunity structure of tropical bats
1. Fragmentation per se due to human land conversion is a landscape-scale phenomenon. Accordingly, assessment of distributional patterns across a suite of potentially connected communities (i.e. metacommunity structure) is an appropriate approach for understanding the effects of landscape modification, and complements the plethora of fragmentation studies that have focused on local community structure. To date, metacommunity structure within human-modified landscapes has been assessed with regard to nestedness along species richness gradients. This is problematic because there is little support that species richness gradients are associated with the factors moulding species distributions. More importantly, many alternative patterns are possible, and different patterns may manifest during different seasons and for different guilds because of variation in resource availability and resource requirements of taxa. 2. We determined the best-fit metacommunity structure of a phyllostomid bat assemblage, frugivore ensemble, and gleaning animalivore ensemble within a human-modified landscape in the Caribbean lowlands of Costa Rica during the dry and wet seasons to elucidate important structuring mechanisms. Furthermore, we identified the landscape characteristics associated with the latent gradient underlying metacommunity structure. 3. We discriminated among multiple metacommunity structures by assessing coherence, range turnover, and boundary clumping of an ordinated site-by-species matrix. We identified the landscape characteristics associated with the latent gradient underlying metacommunity structure via hierarchical partitioning. 4. Metacommunity structure was never nested nor structured along a richness gradient. 5. The phyllostomid assemblage and frugivore ensemble exhibited Gleasonian structure (range turnover along a common gradient) during the dry season and Clementsian structure (range turnover and shared boundaries along a common gradient) during the wet season. Distance between forest patches and forest edge density structured the phyllostomid metacommunity during the dry and wet seasons, respectively. Proportion of pasture and forest patch density structured the frugivore metacommunity during the dry season. 6. Gleaning animalivores exhibited chequerboard structure (mutually exclusive species-pairs) during the dry season and random structure during the wet season. 7. Metacommunity structure was likely mediated by differential resource use or interspecific relationships. Furthermore, the interaction between landscape characteristics and seasonal variation in resources resulted in season-specific and guild-specific distributional patterns.
Data from: Bacterial biophotons as non-local information carriers: species-specific spectral characteristics of a stress response
Studies by Alexander Gurwitsch in the 1920's with onion root cells revealed the phenomenon of mitogenetic radiation. Subsequent works by Popp, Van Wijk, Quickenden, Tillbury and Trushin have demonstrated a link between Gurwitsch's mitogenetic radiation and the biophoton, emissions of light correlated with biological processes. The present study seeks to expand upon these works and explore whether biophoton emissions of bacterial cultures is used as an information carrier of environmental stress. Bacterial cultures (Escherichia coli and Serratia marcescens) were incubated for 24 h in 5 mL of Nutrient Broth to stationary phase and cell densities of ~107 cells/mL. Cultures of E. coli were placed upon a photomultiplier tube housed within a dark box. A second bacterial culture, either E. coli or S. marcescens, was placed in an identical dark box at a distance of 5 m and received injections of hydrogen peroxide. Spectral analyses revealed significant differences in peak frequencies of 7.2, 10.1, and 24.9 Hz in the amplitude modulation of the emitted biophoton signal with respect to whether a peroxide injection occurred or not, and whether the species receiving the injection was E. coli or S. marcescens. These and the subsequent results of discriminant functions suggest that bacteria may release biophotons as a non-local communication system in response to stress, and that these biophotons are species specific.
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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.