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10,812 results for “novels”
Multi-species occupancy modeling provides novel insights into amphibian metacommunity structure and wetland restoration
<p>A fundamental goal of community ecology is to understand species-habitat relationships and how they shape metacommunity structure. Recent advances in occupancy modeling enable habitat relationships to be assessed for both common and rare species within metacommunities using multi-species occupancy models (MSOM). These models account for imperfect species detection and offer considerable advantages over other analytical tools commonly used for community analyses under the elements of metacommunity structure (EMS) framework. Here, we demonstrate that MSOM can be used to infer habitat relationships and test metacommunity theory, using amphibians. Repeated frog surveys were undertaken at 55 wetland sites in eastern Australia. We detected 11 frog species from three families (Limnodynastidae, Myobatrachidae and Pelodryadidae). The rarest species was detected at only one site whereas the most common species was detected at 42 sites (naïve occupancy rate: 0.02 – 0.76). Two models were assessed representing two competing hypotheses; the best-supported model included the covariates distance to the nearest site (connectivity), wetland area, presence of the non-native eastern mosquitofish (<i>Gambusia holbrooki</i>), proportion cover of emergent vegetation, an interaction term between Gambusia and emergent vegetation cover, and the proportion canopy cover over a site. Hydroperiod played no detectable role in metacommunity structure. We found species-habitat relationships that fit with current metacommunity theory – occupancy increased with wetland area and connectivity. There was a strong negative relationship between occupancy and the presence of predatory Gambusia, and a positive interaction between Gambusia and emergent vegetation. The presence of canopy cover strongly increased occupancy for several tree frog species, highlighting the importance of terrestrial habitat for amphibian community structure. We demonstrated how responses by amphibians to environmental covariates at the species level can be linked to occupancy patterns at the metacommunity scale. Our results have clear management implications – wetland restoration projects for amphibians and likely other taxa should maximize wetland area and connectivity, establish partial canopy cover, and eradicate Gambusia or provide aquatic vegetation to mitigate the impact of this non-native fish. We strongly advocate the use of MSOM to elucidate the habitat drivers behind animal occupancy patterns and to derive unbiased occupancy estimates for monitoring programmes.</p>
Genome-wide association results from: Transcriptomic stratification of late-onset Alzheimer's cases reveals novel genetic modifiers of disease pathology
<p>Late-Onset Alzheimer's disease (LOAD) is a common, complex genetic disorder well-known for its heterogeneous pathology. The genetic heterogeneity underlying common, complex diseases poses a major challenge for targeted therapies and the identification of novel disease-associated variants. Case-control approaches are often limited to examining a specific outcome in a group of heterogenous patients with different clinical characteristics. Here, we developed a novel approach to define relevant transcriptomic endophenotypes and stratify decedents based on molecular profiles in three independent human LOAD cohorts. By integrating post-mortem brain gene co-expression data from 2114 human samples with LOAD, we developed a novel quantitative, composite phenotype that can better account for the heterogeneity in genetic architecture underlying the disease. We used iterative weighted gene co-expression network analysis (WGCNA) to reduce data dimensionality and to isolate gene sets that are highly co-expressed within disease subtypes and represent specific molecular pathways. We then performed single variant association testing using whole genome-sequencing data for the novel composite phenotype in order to identify genetic loci that contribute to disease heterogeneity. Distinct LOAD subtypes were identified for all three study cohorts (two in ROSMAP, three in Mayo Clinic, and two in Mount Sinai Brain Bank). Single variant association analysis identified a genome-wide significant variant in <i>TMEM106B</i> (p-value < 5´10<sup>-8</sup>, rs1990620<sup><span><span>G</span></span></sup>) in the ROSMAP cohort that confers protection from the inflammatory LOAD subtype. Taken together,<b> </b>our novel approach can be used to stratify LOAD into distinct molecular subtypes based on affected disease pathways.</p>
Data From: Evaluating the correlation between genome-wide diversity and the release of plastic phenotypic variation in experimental translocations to novel natural environments
<p>Phenotypic reaction norms are often shaped and constrained by selection and are important for allowing organisms to respond to environmental change. However, selection cannot constrain reaction norms for environmental conditions that populations have not experienced. This may allow cryptic neutral genetic variation for the reaction norm to accumulate such that a release of phenotypic variation occurs when it is exposed to novel conditions. Most genomic diversity behaves as if functionally neutral. Genome-wide diversity metrics may therefore correlate with levels of cryptic genetic variation and, as a result, could exhibit a positive relationship with a release of phenotypic variation in novel environments. To test this hypothesis, we conducted translocations of juvenile brook trout (Salvelinus fontinalis) from 12 populations to novel uninhabited ponds that represented a gradient of environmental conditions. We assessed reaction norms for morphological traits (body size and four morphometric relative warps) across pond environmental gradients and evaluated the effect of genome-wide heterozygosity on phenotypic variability. All traits displayed plastic reaction norms. Overall, we found some evidence that a release of phenotypic variation consistent with cryptic genetic variation can occur in novel environmental conditions. However, the extent to which this release was correlated with average genome-wide diversity was limited to only one of five morphological traits examined. Our results suggest that the link between genomic diversity and the accumulation of cryptic genetic variation in reaction norms may be limited. Similarly, reaction norms were constrained for many of the morphological traits examined. Past conditions may have constrained reaction norms in the putatively novel environments despite significant deviations from contemporary source population habitat. Additionally, as a generalist colonizing species brook trout may exhibit plastic phenotypes across a wide range of environmental conditions.</p>
Data from: Phylogenomics reveals novel relationships among Neotropical crocodiles (Crocodylus spp.)
<p>Extant species in the order Crocodylia are remnants of an ancient lineage of large-bodied archosaur reptiles. Despite decades of systematic studies, phylogenetic relationships among members of the genus <i>Crocodylus</i> (true crocodiles) in the Neotropics are poorly understood. Here we estimated phylogenomic relationships among the four extant <i>Crocodylus </i>species in the Americas. Species-tree reconstructions using genotypic data from 17,538 SNPs collected for 33 individuals spanning six <i>Crocodylus </i>species (four ingroup and two outgroup) revealed novel relationships for all Neotropical species. For the first time, <i>C. acutus</i>, the American crocodile, was recovered as monophyletic when individuals from Antillean and continental populations were analyzed together. Our results also contradict previous inferences based on mitochondrial DNA data and a limited number of nuclear markers by robustly grouping Morelet's crocodile (<i>C. moreletii</i>) as the sister species to <i>C. acutus</i>., suggesting a novel phylogeographic hypothesis for the group. The present study punctuates the importance of using nuclear genome-wide information and representative sampling for resolving phylogenetic relationships, especially in broadly distributed species and those with complex evolutionary histories.</p>
Conspicuous animal signals avoid the cost of predation by being intermittent or novel: confirmation in the wild using hundreds of robotic prey
<p>Social animals are expected to face a trade-off between producing a signal that is detectible by mates and rivals, but not obvious to predators. This trade-off is fundamental for understanding the design of many animal sig- nals, and is often the lens through which the evolution of alternative communication strategies is viewed. We have a reasonable working knowl- edge of how conspecifics detect signals under different conditions, but how predators exploit conspicuous communication of prey is complex and hard to predict. We quantified predation on 1566 robotic lizard prey that per- formed a conspicuous visual display, possessed a conspicuous ornament or remained cryptic. Attacks by free-ranging predators were consistent across two contrasting ecosystems and showed robotic prey that performed a conspicuous display were equally likely to be attacked as those that remained cryptic. Furthermore, predators avoided attacking robotic prey with a fixed, highly visible ornament that was novel at both locations. These data show that it is prey familiarity—not conspicuousness—that determine predation risk. These findings replicated across different preda- tor–prey communities not only reveal how conspicuous signals might evolve in high predation environments, but could help resolve the paradox of aposematism and why some exotic species avoid predation when invad- ing new areas.</p>
Image stack, PLY-files and a NEX-file accompanying: A new symmoriiform from the Late Devonian of Morocco: novel jaw function in ancient sharks
<p>We describe the small chondrichthyan Ferromirum oukherbouchi n.gen. et sp. from the Famennian (Late Devonian) of the Maïder region in Morocco. This chondrichthyan is exceptionally well preserved and displays not only mineralized soft tissues but also undeformed cartilages of the head, gills, and shoulder girdle. A reconstruction of the head using 3D-prints revealed a previously unknown kind of jaw articulation. Here, we make the original cropped image stack and PLY-files of the single cartilaginous elements accessible. Additionally, a nexus-file with the character matrix used for the cladogram shown in the article is included.</p>
Synthesis of a novel amphoteric copolymer and its application as a dispersant for coal water slurry preparation
<p>In this work, a novel amphoteric copolymer was synthesized via free radical polymerization, named Poly(sodium p-styrenesulfonate–co-acrylic acid-co-diallyldimethylammonium chloride) (P(SS-co-AA-co-DMDAAC)). Afterwards, P(SS-co-AA-co-DMDAAC) was explored for use as a dispersant in coal water slurry (CWS) preparation. The structure of P(SS-co-AA-co-DMDAAC) was verified by Fourier transform infrared spectroscopy (FTIR) and Nuclear magnetic resonance (NMR). The synthetic conditions were optimized as the feed ratio of AA to SS was 1:1 (for Yulin coal) or 1.5:1 (for Yili coal), and DMDAAC dosage was 4.0 wt% (for Yulin coal) and 6.0 wt% (for Yili coal) toward total monomers. The performances of P(SS-co-AA-co-DMDAAC) as a dispersant for CWS were evaluated by various technologies, such as apparent viscosity, Zeta potential, static stability and contact angle measurements. The results revealed that the optimized dosage of P(SS-co-AA-co-DMDAAC) in CWS preparation was 0.3 wt% and 0.4 wt% for Yulin coal and Yili coal respectively. In this optimum condition, CWS prepared using P(SS-co-AA-co-DMDAAC) as dispersant showed a typical shear thinning behavior and excellent stability, which are desired in industry. The rheological models also confirmed the pseudo-plastic characteristics of CWS. Finally, as compared to the widespread used anionic dispersant Poly(sodium p-styrenesulfonate) (PSS), P(SS-co-AA-co-DMDAAC) developed in this work exhibited better slurry making performance. Introduction of cationic functional groups promoted the adsorption of dispersant, which further enhanced the electrostatic repulsion among coal particles. Accordingly, the viscosity of CWS decreased and static stability enhanced.</p>
Novel multiplex TaqMan assay for differentiation of the four major pathogenic Brachyspira species in swine
<p>Table S1</p> <p>503 Brachyspira samples used for validation of the novel 5-plex qPCR assay and comparison of results obtained by four independent PCR assays</p>
Novel Science communication – how to build public health knowledge across the social gradient. The Healthy Choices Project (WP5).
<p>Everyday life consists of hundreds of choices of which many may have an impact on our health. The citizens of the modern Nordic welfare states are in general well-educated and thus can be assumed to know what is best for them. Despite this our health care systems face an increasing burden of lifestyle related diseases and there is a difference across the social gradient. Here building public health knowledge through communication is key. The reason for people making unhealthy choices are many and can be that; they do not know what is good for them (lack information) or do not understand (lack understanding) or do not care (carelessness). However it seems likely that it is more complex than that. Maybe they do not receive the information, because gets conveyed through channels that they do not consult or maybe the format of the message does not ‘click’? Could it be, that ‘one media message or channel does not fit all’? </p> <p>Over the last decades there has been an increased focus from both scientists themselves and politicians to scientific and practical field of ‘science communication’. Consequently, various advanced modes of communicating e.g. health issues to the general populations have been developed, and today scholars of Mass Media term this development the ‘scientification’ of media. Furthermore, media and information availability has exploded since the emergence of the Internet in the early 1990s. Research has indicated that social gradient also is a factor affecting a person’s media consumption and habit. </p> <p>In the healthy choices project we aim through novel methods to learn more about these challenges and at the develop new methods of conveying public health knowledge to enable people to make healthier choices across the social gradient. We have so far built a framework for this including a science group, consisting of public health experts, and a communication group consisting of experienced science communicators. The Science group is consulted about risk factors and health endpoints and what to prioritize. Two PhD students will be involved in; 1) assessing media consumption and usage related to health issues across social classes (Low social gradient versus high social gradient) and across the generational gap (young and elderly) and 2) develop and test various media message formats for target groups including considerations of the social gradient. This project will provide new understanding on how to communicate public health messages and reduce social inequalities in health.</p> <p> </p>
Data from: Adaptive evolution to novel predators facilitates the evolution of damselfly species range shifts
Most species have evolved adaptations to reduce the chances of predation. In many cases adaptations to coexist with one predator generate tradeoffs in the ability to live with other predators. Consequently, the ability to live with one predator may limit the geographic distributions of species, such that adaptive evolution to coexist with novel predators may facilitate range shifts. In a case study with Enallagma damselflies, we used a comparative phylogenetic approach to test the hypothesis that adaptive evolution to live with a novel predator facilitates range size shifts. Our results suggest that the evolution of Enallagma shifting from living in ancestral lakes with fish as top predators, to living in lakes with dragonflies as predators, may have facilitated an increase in their range sizes. This increased range size likely arose because lakes with dragonflies were widespread, but unavailable as a habitat throughout much of the evolutionary history of Enallagma because they were historically maladapted to coexist with dragonfly predators. Additionally, the traits that have evolved as defenses against dragonflies also likely enhanced damselfly dispersal abilities. While many factors underlie the evolutionary history of species ranges, these results suggest a role for the evolution of predator-prey interactions.
A single-parasite transcriptional atlas of Toxoplasma gondii reveals novel control of antigen expression
Toxoplasma gondii, a protozoan parasite, undergoes a complex and poorly understood developmental process that is critical for establishing a chronic infection in its intermediate hosts. Here, we applied single-cell RNA-sequencing (scRNA-seq) on >5,400 Toxoplasma in both tachyzoite and bradyzoite stages using three widely studied strains to construct a comprehensive atlas of cell-cycle and asexual development, revealing hidden states and transcriptional factors associated with each developmental stage. Analysis of SAG1-related sequence (SRS) antigenic repertoire reveals a highly heterogeneous, sporadic expression pattern unexplained by measurement noise, cell cycle, or asexual development. Furthermore, we identified AP2 IX-1 as a transcription factor that controls the switching from the ubiquitous SAG1 to rare surface antigens not previously observed in tachyzoites. In addition, comparative analysis between Toxoplasma and Plasmodium scRNA-seq results reveals concerted expression of gene sets, despite fundamental differences in cell division. Lastly, we built an interactive data-browser for visualization of our atlas resource.
Changes in multiple environmental factors additively enhance the dominance of an exotic plant with a novel trade-off pattern
<p>1. Whether global changes impact native and exotic species differently is unclear, because the changes may favour both native and exotic species over competitors. Previous studies have mainly focused on the separate effects of the different environmental changes, but plant communities are influenced by changes in multiple environmental factors, and it is still unclear whether native and exotic species respond similarly to the combined effects of these factors.</p> <p>2. We hypothesized that differences in interspecific trade-offs between native and exotic species could lead to the dominance of exotic species when the species are simultaneously subjected to multiple environmental changes.</p> <p>3. Using coastal saltmarsh plant communities as the study system, we experimentally manipulated flooding and nutrient enrichment, examined the interspecific trade-offs between competitiveness and stress tolerance for two native and one exotic species, and explored the combined effect of the two environmental changes on both native–native and native–exotic species interactions.</p> <p>4. We found that flooding and nutrient enrichment oppositely affected native–native species interactions but additively affected native–exotic species interactions. The two factors together resulted in no net change in the relative advantages between the two native species but enhanced the dominance of the exotic species over the native species. This disparity occurred because the exotic species was not subject to the interspecific trade-off between competitiveness and stress tolerance that constrained the native species.</p> <p>5. <i><b>Synthesis</b></i>. Our results suggest that changes in multiple environmental factors favour exotic species because of evolutionary novel trade-off patterns. Mechanisms underlying species coexistence in the invaded community such as interspecific trade-offs should be considered when researchers attempt to predict the effects of global changes on biological invasions.</p>
Data from: The shape of avian eggs: assessment of a novel metric for quantifying eggshell conicality
<p>Studying avian egg shape and other aspects of its morphology has recently undergone a renaissance. Yet, most studies rely solely on two metrics for the quantification of egg shape: elongation and asymmetry. The difficulty of additionally quantifying the curvature of an eggshell has yielded many attempts including those with complex equations and spatial modeling techniques based on digitized images. These have lacked an independent single-variable metric, hampering comparative studies. We propose a metric for one common quality of egg shape, conicality, which is notably variable in diverse species' calcareous shells including shorebirds and non-avian theropods. This metric utilizes multiple measurements of the slope along an eggs profile to produce a distribution of angular measurements, which can be analyzed with a Kurtosis (K) value. This metric was tested with sets of computer modeled and 3D printed egg forms, where elongation, the percentage of conicality, and the relative curvature of the shell profile were controlled. For applicability to natural eggs and their diversity across taxa, the Kurtosis value was used to quantify the gradient of conicality across a focal avian family, Alcidae, where the Kurtosis value successfully identified the most conical eggs using qualitative descriptions from well-established literature. Given the significance of egg morphology and profile curvature to structural integrity, surface-area to volume ratio, egg mobility/stability, nesting behavior, and embryonic development, our proposed measure of conicality could prove a useful variable to the study of avian and non-avian egg-producing species. </p>
Novel Tests of the Key Innovation Hypothesis: Adhesive Toepads in Arboreal Lizards
Abstract The evolution of key innovations—unique features that enable a lineage to interact with the environment in a novel way—may drive broad patterns of adaptive diversity. However, traditional tests of the key innovation hypothesis, those which attempt to identify the evolutionary effect of a purported key innovation by comparing patterns of diversity between lineages with and without the key trait, have been challenged on both conceptual and statistical grounds. Here, we explore alternative, untested hypotheses of the key innovation framework. In lizards, adhesive toepad structures increase grip strength on vertical and smooth surfaces such as tree trunks and leaves and have independently evolved multiple times. As such, toepads have been posited as a key innovation for the evolution of arboreality. Leveraging a habitat use dataset applied to a global phylogeny of 2692 lizard species, we estimated multiple origins of toepads in three major clades and more than 100 origins of arboreality widely across the phylogeny. Our results suggest that toepads arise adaptively in arboreal lineages and are subsequently rarely lost while maintaining arboreal ecologies. Padless lineages transition away from arboreality at a higher rate than those with toepads, and high rates of invasion of arboreal niches by non-arboreal padbearing lineages provides further evidence that toepads may be a key to unlocking evolutionary access to the arboreal zone. Our results and analytical framework provide novel insights to understand and evaluate the ecological and evolutionary consequences of key innovations.
Characterisation of protease activity duringSARS-CoV-2 infection identifies novel viralcleavage sites and cellular targets withtherapeutic potential
<p><strong>Virus infections in siRNA-based cellular protein knockdowns - imaging dataset for cell viability</strong><br> Host proteins were knocked-down in A549-Ace2 cells using specific dsiRNAs from IDT. Briefly, A549-Ace2 cells seeded at 1x10$^{4}$ cells/well in 96-well plates. After 24 hours, each well was transfected with 5 pmol of individual dsiRNAs using Lipofectamine RNAiMAX (Thermo Fisher Scientific) according to the manufacturer’s instructions. 24 hours post transfection, the cell culture supernatant was removed and replaced with virus inoculum (MOI of 0.1 PFU/cell). Following a 1 hour adsorption at 37°C, the virus inoculum was removed and replaced with fresh 2\% FBS/DMEM media. Cells were incubated at 37°C for 3 days before supernatants were harvested. Samples were either heat-inactivated at 80°C for 20 min and viral RNA was quantified by RT-qPCR, using previously published SARS-CoV-2 specific primers targeting the N gene \cite{ChuClinChem}. RT-qPCR was performed using the Luna Universal One-Step RT-qPCR Kit (NEB) in an Applied Biosystems QuantStudio 7 thermocycler, using the following cycling conditions: 55 °C for 10 min, 95 °C for 1 min, and 40 cycles of 95 °C for 10 sec, followed by 60 °C for 1 min. The quantity of viral genomes is expressed as PFU equivalents, and was calculated by performing a standard curve with RNA derived from a viral stock with a known viral titer. Alternatively, infectious virus titers were quantified using plaque assays as described above.</p> <p>To quantify siRNA-based cellular protein knockdowns, A549-Ace2 cells were seeded and transfected with individual dsiRNAs as described above. After 24 hours incubation at 37 °C cells were lysed and RNA was extracted using Trizol (ThermoFisher Scientific) followed by purification using the Direct-zol-96 RNA extraction kit (Zymo) following the manufacturer’s instructions. RNA levels of target proteins were subsequently quantified by using RT-with the Luna Universal One-Step RT-qPCR Kit (NEB) in an Applied Biosystems QuantStudio 7 thermocycler using gene-specific primers. Expression levels were compared to scrambled dsiRNA-transfected cells und normalized to expression of human beta-actin. Knockdown efficiencies were calculated using ΔΔCt in Matlab. </p> <p>To assess cell viability after siRNA knockdowns, cells were seeded and transfected as described above. 24 hours after transfection cell viability was measured using alamarBlue reagent (ThermoFisher Scientific), media was removed and replaced with alamarBlue and incubated for 1h at 37 °C and fluorescence measured in a Tecan Infinite M200 Pro plate reader. Percentage viability was calculated relative to untreated cells (100\% viability) and cells lysed with 20\% ethanol (0\% viability), included in each plate.</p> <p>For cell counting to determine cell numbers, cells were fixed in formalin to deactivate virus. The fixed cells were stained with 5µg/ml of Hoechst 33258 (Sigma). The assay plates were imaged on an IX-83 automated inverted microscope (Olympus) using a 10x objective. The DAPI settings (Ex UV 377/50, Em 415–480) were used to image Hoechst 33258. The acquisition setup was configured to image 4 sites per well. The nuclei were identified using the object detection module in the ScanR analysis software.</p> <p> </p> <p>Data provided in two zip files. Sample layout/key within the plates is provided within the zip files.</p>
Comparing raccoon MHC diversity in native and introduced ranges: evidence for the importance of functional immune diversity for adaptation and survival in novel environments.
<p>The adaptive potential of invasive species is related to the genetic <span class="il">diversity</span> of the invader, which is influenced by genetic drift and natural selection. Typically, the genetic <span class="il">diversity</span> of invaders is studied with neutral genetic markers, however, the expectation of reduced <span class="il">diversity</span> has not been consistently supported by empirical studies. Here, we describe and interpret genetic <span class="il">diversity</span> at both neutral microsatellite loci and the immune related <span class="il">MHC</span>-DRB locus of <span class="il">native</span> and invasive populations of <span class="il">raccoon</span> to better understand of how drift and selection impact patterns of genetic <span class="il">diversity</span> during the invasion process. We found that despite the loss of many <span class="il">MHC</span> alleles in comparison with <span class="il">native</span> populations, functional <span class="il">MHC</span> supertypes are preserved in the invasive region. In the <span class="il">native</span> <span class="il">raccoon</span> population the number of supertypes within individuals was higher than expected under a neutral model. The high level of individual functional divergence may facilitate the adaptation to local conditions in the invasive range. These results suggest that selection is driving divergent allele combinations despite drift causing allelic loss. In the invasive populations, we also detected increased population structure at microsatellites compared to the <span class="il">MHC</span> locus, further suggesting that balancing selection is acting on adaptively important regions of the <span class="il">raccoon</span> genome. Finally, we found that alleles known to exhibit resistance to rabies in the <span class="il">native</span> range, Prlo-DRB*4, Prlo-DRB*16 and Prlo-DRB*102, were the most common alleles in the European populations, suggesting directional selection is acting on this locus. Our research shows empirical support for the importance of functional immune <span class="il">diversity</span> for adaptation and survival in novel environments.</p>
Data from: Museum specimens provide novel insights into changing plant-herbivore interactions
Mounting evidence shows that species interactions may mediate how individual species respond to climate change. However, long-term anthropogenic effects on species interactions are poorly characterized due to a lack of data. Insect herbivory is a major ecological process that represents the interaction between insect herbivores and their host plants, but historical data on insect damage to plants is particularly sparse. Here, we suggest that museum collections of insects and plants can fill key gaps in our knowledge on changing trophic interactions, including proximate mechanisms and the net outcomes of multiple global change drivers across diverse insect herbivore-plant associations. We outline theory on how global change may affect herbivores and their host plants and highlight the unique data that could be extracted from museum specimens to explore their shifting interactions. We aim to provide a framework for using museum specimens to explore how some of the most diverse co-evolved relationships are responding to climate and land use change.
Data from: A novel approach to wildlife transcriptomics provides evidence of disease-mediated differential expression and changes to the microbiome of amphibian populations
Ranaviruses are responsible for a lethal, emerging infectious disease in amphibians and threaten their populations throughout the world. Despite this, little is known about how amphibian populations respond to ranaviral infection. In the United Kingdom, ranaviruses impact the common frog (Rana temporaria). Extensive public engagement in the study of ranaviruses in the UK has led to the formation of a unique system of field sites containing frog populations of known ranaviral disease history. Within this unique natural field system, we used RNA sequencing (RNA-Seq) to compare the gene expression profiles of R. temporaria populations with a history of ranaviral disease and those without. We have applied a RNA read filtering protocol that incorporates Bloom filters, previously used in clinical settings, to limit the potential for contamination that comes with the use of RNA-Seq in non-laboratory systems. We have identified a suite of 407 transcripts that are differentially expressed between populations of different ranaviral disease history. This suite contains genes with functions related to immunity, development, protein transport and olfactory reception amongst others. A large proportion of potential non-coding RNA transcripts present in our differentially expressed set provides first evidence of a possible role for long non-coding RNA (lncRNA) in amphibian response to viruses. Our read-filtering approach also removed significantly more bacterial reads from libraries generated from postitive disease history populations. Subsequent analysis revealed these bacterial read sets to represent distinct communities of bacterial species, which is suggestive of an interaction between ranavirus and the host microbiome in the wild.
Data from: A novel method to analyze social transmission in chronologically sequenced assemblages, implemented on cultural inheritance of the art of cooking
Here we present an analytical technique for the measurement and evaluation of changes in chronologically sequenced assemblages. To illustrate the method, we studied the cultural evolution of European cooking as revealed in seven cook books dispersed over the past 800 years. We investigated if changes in the set of commonly used ingredients were mainly gradual or subject to fashion fluctuations. Applying our method to the data from the cook books revealed that overall, there is a clear continuity in cooking over the ages – cooking is knowledge that is passed down through generations, not something (re-)invented by each generation on its own. Looking at three main categories of ingredients separately (spices, animal products and vegetables), however, disclosed that all ingredients do not change according to the same pattern. While choice of animal products was very conservative, changing completely sequentially, changes in the choices of spices, but also of vegetables, were more unbounded. We hypothesize that this may be due a combination of fashion fluctuations and changes in availability due to contact with the Americas during our study time period. The presented method is also usable on other assemblage type data, and can thus be of utility for analyzing sequential archaeological data from the same area or other similarly organized material.
Data from: Novel sources of (co)variation in nestling begging behavior and hunger at different biological levels of analysis
<p>Biological hypotheses predicting patterns of offspring begging typically concern the covariance with hunger and/or development at specific hierarchical levels. For example, hunger drives within-individual patterns of begging, but begging also drives food intake among individuals within broods, and begging and food intake can covary positively or negatively among genotypes or broods. Testing biological phenomena that occur at multiple levels therefore requires the partitioning of covariance between traits of interest to ensure that each level-specific relationship is appropriately assessed. We performed a partial cross-fostering study on a wild population of great tits (Parus major), then used multivariate mixed-models to partition variation and covariation in nestling begging effort and two metrics of nestling hunger within versus among individual nestlings and broods. At the within-individual level, we found that nestlings begged more intensely when hungrier (positive correlation between begging and hunger). However, among individuals, nestlings that were fed more frequently also begged more intensely on average (negative correlation between begging and hunger). Variation in nestling mass did not give rise to the negative correlation between begging and hunger among nestlings, but we did find that lighter nestlings begged more intensely than their heavier biological siblings, suggesting that this effect may be driven by a genetic component linked to offspring size. Our study illustrates how patterns of covariance can differ across biological levels of analysis and addresses biological mechanisms that could produce these previously obscured patterns.</p>
ScienceDex guides
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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.