Find research datasets worth reusing

Data from: Regulation of transposable elements: interplay between TE-encoded regulatory sequences and host-specific trans-acting factors in Drosophila melanogaster

Transposable elements (TEs) are mobile genetic elements that can move around the genome, and their expression is one precondition for this mobility. Because the insertion of TEs in new genomic positions is largely deleterious, the molecular mechanisms for transcriptional suppression have been extensively studied. In contrast, very little is known about their primary transcriptional regulation. Here, we characterize the expression dynamics of TE families in Drosophila melanogaster across a broad temperature range (13–29°C). In 71% of the expressed TE families, the expression is modulated by temperature. We show that this temperature-dependent regulation is specific for TE families and strongly affected by the genetic background. We deduce that TEs carry family-specific regulatory sequences, which are targeted by host-specific trans-acting factors, such as transcription factors. Consistent with the widespread dominant inheritance of gene expression, we also find the prevailing dominance of TE family expression. We conclude that TE family expression across a range of temperatures is regulated by an interaction between TE family-specific regulatory elements and trans-acting factors of the host.

Data from: Understanding the spectacular failure of DNA barcoding in willows (Salix): Does this result from a trans-specific selective sweep?

Willows (Salix: Salicaceae) form a major ecological component of Holarctic floras, and consequently are an obvious target for a DNA-based identification system. We surveyed two to seven plastid genome regions (~3.8 kb; ~3% of the genome) from 71 Salix species across all five subgenera, to assess their performance as DNA barcode markers. Although Salix has a relatively high level of interspecific hybridization, this may not sufficiently explain the near complete failure of barcoding that we observed: only one species had a unique barcode. We recovered 39 unique haplotypes, from more than 500 specimens, that could be partitioned into six major haplotype groups. A unique variant of group I (haplotype 1*) was shared by 53 species in three of five Salix subgenera. This unusual pattern of haplotype sharing across infrageneric taxa is suggestive of either a massive non-random coalescence failure (incomplete lineage sorting), or of repeated plastid capture events, possibly including a historical selective sweep of haplotype 1* across taxonomic sections. The former is unlikely as molecular dating indicates that haplotype 1* originated recently, and is nested in the oldest major haplotype group in the genus. Further, we detected significant non-neutrality in the frequency spectrum of mutations in group I, but not outside group I, and demonstrated a striking absence of geographic structure to the haplotype distributions in this group. The most likely explanation for the patterns we observed involves recent repeated plastid capture events, aided by widespread hybridization and long-range seed dispersal, but primarily propelled by one or more trans-species selective sweeps.

opencc-zeroNov 2019View details →

Mapping the EORTC QLQ-C30 and QLQ-H&N35 to the EQ-5D for head and neck cancer: can disease-specific utilities be obtained?

Introduction Innovations in head and neck cancer (HNC) treatment are often subject to economic evaluation prior to their reimbursement and subsequent access for patients. Mapping functions facilitate economic evaluation of new treatments when the required utility data is absent, but quality of life data is available. The objective of this study is to develop a mapping function translating the EORTC QLQ-C30 to EQ-5D-derived utilities for HNC through regression modeling, and to explore the added value of disease-specific EORTC QLQ-H&N35 scales to the model. Methods Data was obtained on patients with primary HNC treated with curative intent derived from two hospitals. Model development was conducted in two phases: 1. Predictor selection based on theory- and data-driven methods, resulting in three sets of potential predictors from the quality of life questionnaires; 2. Selection of the best out of four methods: ordinary-least squares, mixed-effects linear, Cox and beta regression, using the first set of predictors from EORTC QLQ-C30 scales with most correspondence to EQ-5D dimensions. Using a stepwise approach, we assessed added values of predictors in the other two sets. Model fit was assessed using Akaike and Bayesian Information Criterion (AIC and BIC) and model performance was evaluated by MAE, RMSE and limits of agreement (LOA). Results The beta regression model showed best model fit, with global health status, physical-, role- and emotional functioning and pain scales as predictors. Adding HNC-specific scales did not improve the model. Model performance was reasonable; R2=0.39, MAE=0.0949, RMSE=0.1209, 95% LOA of -0.243 to 0.231 (bias -0.01), with an error correlation of 0.32. The estimated shrinkage factor was 0.90. Conclusions Selected scales from the EORTC QLQ-C30 can be used to estimate utilities for HNC using beta regression. Including EORTC QLQ-H&N35 scales does not improve the mapping function. The mapping model may serve as a tool to enable cost-effectiveness analyses of innovative HNC treatments, for example for reimbursement issues. Further research should assess the robustness and generalizability of the function by validating the model in an external cohort of HNC patients.

Data from: Differences in thallus chemistry are related to species-specific effects of biocrust-forming lichens on soil nutrients and microbial communities

1. It is well-known that vascular plants have species-specific effects on soil properties. However, little is known on how individual species forming biocrusts, communities dominated by lichens, mosses and cyanobacteria that are prevalent in many ecosystems world-wide, affect microbial communities and soil variables related to nutrient cycling. 2. We evaluated the relationship of six biocrust-forming lichens (Buellia epipolia, Diploschistes diacapsis, Fulgensia subbracteata, Psora decipiens, Squamarina cartilaginea and Squamarina lentigera) with microbial abundance and multiple variables associated with soil nitrogen (N), carbon (C) and phosphorus (P) cycling and storage. We also evaluated whether the composition of lichen tissues (contents in C, N, P and polyphenols) is related to the C, N, P availability and microbial abundance in soils. Finally, we assessed what lichen species positively and negatively relate to soil fertility compared to bare ground areas without biocrusts. 3. We found contrasted C, N, P availability and soil microbial abundance under the different biocrust-forming lichens. Interestingly, inorganic P and amino acids were the most important factors differentiating lichen microsites. These differences in nutrient availability seem to be related to the C, N and P composition of the lichen tissues. For example, soils under D. diacapsis and P. decipiens, which had the lowest and highest C, N and P contents in their tissues, respectively, had the lowest and highest nutrient availability, respectively. We also found contrasted soil microbes abundance under the different soil lichens. For instance, F. subbracteata and D. diacapsis were negatively related to the abundance of bacteria compared to bare ground areas. 4. Our results support the idea that, as found with vascular plants, biocrust-forming lichens have species-specific effects on soil microbial communities and C, N and P cycling. Thus, continuing considering biocrusts as a unique entity will only add confusion to our knowledge of how they control nutrient availability and microbial abundance in the ecosystems where this key community is prevalent.

Data from: Myelin basic protein induces neuron-specific toxicity by directly damaging the neuronal plasma membrane

The central nervous system (CNS) insults may cause massive demyelination and lead to the release of myelin-associated proteins including its major component myelin basic protein (MBP). MBP is reported to induce glial activation but its effect on neurons is still little known. Here we found that MBP specifically bound to the extracellular surface of the neuronal plasma membrane and induced neurotoxicity in vitro. This effect of MBP on neurons was basicity-dependent because the binding was blocked by acidic lipids and competed by other basic proteins. Further studies revealed that MBP induced damage to neuronal membrane integrity and function by depolarizing the resting membrane potential, increasing the permeability to cations and other molecules, and decreasing the membrane fluidity. At last, artificial liposome vesicle assay showed that MBP directly disturbed acidic lipid bilayer and resulted in increased membrane permeability. These results revealed that MBP induces neurotoxicity through its direct interaction with acidic components on the extracellular surface of neuronal membrane, which may suggest a possible contribution of MBP to the pathogenesis in the CNS disorders with myelin damage.

opencc-zeroDec 2018View details →

Data from: Landscape-specific thresholds in the relationship between species richness and natural land cover

1. Thresholds in the relationship between species richness and natural land cover can inform landscape-level vegetation protection and restoration targets. However, landscapes differ considerably in composition and other environmental attributes. If the effect of natural land cover on species richness depends on (i.e. interacts with) these attributes, and this affects the value of thresholds in this relationship, such dependencies must be considered when using thresholds to guide landscape management. 2. We hypothesised that the amount of natural land cover at which a threshold occurs would differ in predictable ways with particular anthropogenic, abiotic and biotic attributes of landscapes. To test this, we related woodland bird species richness in 251 landscapes, each 100 km 2, to natural land cover in south-east Australia. We compared the fit of exponential and threshold models of the richness-natural land cover relationship, focussing on the extent of natural land cover at which thresholds presented among landscapes that differed in matrix land use intensity, heterogeneity, productivity and the prevalence of strong biotic interactors. We used linear mixed modelling to examine how interactions between natural land cover and the various landscape attributes affected the fit of models of species richness. 3. Threshold models of the richness-natural land cover relationship were always a better fit than exponential models. Threshold values did not vary consistently with specific landscape attributes, with the exception of landscapes that were classified by the prevalence of strong biotic interactors (hypercompetitive native birds of the genus Manorina). 4. Natural land cover had a more positive effect on species richness in landscapes when Manorina prevalence was higher. This positive interaction provided the biggest improvement in explanatory power of models of species richness. 5. Synthesis and applications. While we detected an interaction between Manorina prevalence and the area of natural land cover, generalities relating to the underlying nature of thresholds in the richness-natural land cover relationship remain elusive. Complex interactions, relating to various landscape attributes and associated ecological processes, likely underpin variation in threshold values. Until these complexities are better understood, the use of thresholds for informing landscape management and conservation target setting should be approached with caution.

Data from: Paired-end analysis of transcription start sites in Arabidopsis reveals plant-specific promoter signatures

Understanding plant gene promoter architecture has long been a challenge due to the lack of relevant large-scale data sets and analysis methods. Here, we present a publicly available, large-scale transcription start site (TSS) data set in plants using a high-resolution method for analysis of 5′ ends of mRNA transcripts. Our data set is produced using the paired-end analysis of transcription start sites (PEAT) protocol, providing millions of TSS locations from wild-type Columbia-0 Arabidopsis thaliana whole root samples. Using this data set, we grouped TSS reads into "TSS tag clusters" and categorized clusters into three spatial initiation patterns: narrow peak, broad with peak, and weak peak. We then designed a machine learning model that predicts the presence of TSS tag clusters with outstanding sensitivity and specificity for all three initiation patterns. We used this model to analyze the transcription factor binding site content of promoters exhibiting these initiation patterns. In contrast to the canonical notions of TATA-containing and more broad "TATA-less" promoters, the model shows that, in plants, the vast majority of transcription start sites are TATA free and are defined by a large compendium of known DNA sequence binding elements. We present results on the usage of these elements and provide our Plant PEAT Peaks (3PEAT) model that predicts the presence of TSSs directly from sequence.

opencc-zeroDec 2012View details →

Data from: Genome-wide association study identifies vitamin B5 biosynthesis as a host specificity factor in Campylobacter

Genome-wide association studies have the potential to identify causal genetic factors underlying important phenotypes but have rarely been performed in bacteria. We present an association mapping method that takes into account the clonal population structure of bacteria and is applicable to both core and accessory genome variation. Campylobacter is a common cause of human gastroenteritis as a consequence of its proliferation in multiple farm animal species and its transmission via contaminated meat and poultry. We applied our association mapping method to identify the factors responsible for adaptation to cattle and chickens among 192 Campylobacter isolates from these and other host sources. Phylogenetic analysis implied frequent host switching but also showed that some lineages were strongly associated with particular hosts. A seven-gene region with a host association signal was found. Genes in this region were almost universally present in cattle but were frequently absent in isolates from chickens and wild birds. Three of the seven genes encoded vitamin B5 biosynthesis. We found that isolates from cattle were better able to grow in vitamin B5-depleted media and propose that this difference may be an adaptation to host diet.

Data from: Species-specific differences in adaptive phenotypic plasticity in an ecologically relevant trophic trait: hypertrophic lips in Midas cichlid fishes

The spectacular species richness of cichlids and their diversity in morphology, coloration, and behaviour have made them an ideal model for the study of speciation and adaptive evolution. Hypertrophic lips evolved repeatedly and independently in African and Neotropical cichlid radiations. Cichlids with hypertrophic lips forage predominantly in rocky crevices and it has been hypothesized that mechanical stress caused by friction could result in larger lips through phenotypic plasticity. To test the influence of the environment on the size and development of lips, we conducted a series of breeding and feeding experiments on Midas cichlids. Full-sibs of Amphilophus labiatus (thick-lipped) and A. citrinellus (thin-lipped) each were split into a control group which was fed food from the water column and a treatment group whose food was fixed to substrates. We found strong evidence for phenotypic plasticity on lip area in the thick-lipped species, but not in the thin-lipped species. Intermediate phenotypic values were observed in hybrids from thick- and thin-lipped species reared under "control" conditions. Thus, both a genetic, but also a phenotypic plastic component is involved in the development of hypertrophic lips in Neotropical cichlids. Moreover, species-specific adaptive phenotypic plasticity was found, suggesting that plasticity is selected for in recent thick-lipped species.

opencc-zeroDec 2014View details →

Data from: Barcoding the kingdom Plantae: new PCR primers for ITS regions of plants with improved universality and specificity

The internal transcribed spacer (ITS) of nuclear ribosomal DNA is one of the most commonly used DNA markers in plant phylogenetic and DNA barcoding analyses, and it has been recommended as a core plant DNA barcode. Despite this popularity, the universality and specificity of PCR primers for the ITS region are not satisfactory, resulting in amplification and sequencing difficulties. By thoroughly surveying and analysing the 18S, 5.8S and 26S sequences of Plantae and Fungi from GenBank, we designed new universal and plant-specific PCR primers for amplifying the whole ITS region and a part of it (ITS1 or ITS2) of plants. In silico analyses of the new and the existing ITS primers based on these highly representative data sets indicated that (i) the newly designed universal primers are suitable for over 95% of plants in most groups; and (ii) the plant-specific primers are suitable for over 85% of plants in most groups without amplification of fungi. A total of 335 samples from 219 angiosperm families, 11 gymnosperm families, 24 fern and lycophyte families, 16 moss families and 17 fungus families were used to test the performances of these primers. In vitro PCR produced similar results to those from the in silico analyses. Our new primer pairs gave PCR improvements up to 30% compared with common-used ones. The new universal ITS primers will find wide application in both plant and fungal biology, and the new plant-specific ITS primers will, by eliminating PCR amplification of nonplant templates, significantly improve the quality of ITS sequence information collections in plant molecular systematics and DNA barcoding.

Data from: Estimating parent-specific QTL effects through cumulating linked identity-by-state SNP effects in multiparental populations

The emergence of multiparental mapping populations enabled plant geneticists to gain deeper insights into the genetic architecture of major agronomic traits and to map quantitative trait loci (QTLs) controlling the expression of these traits. Although the investigated mapping populations are similar, one open question is whether genotype data should be modelled as identical by state (IBS) or identical by descent (IBD). Whereas IBS simply makes use of raw genotype scores to distinguish alleles, IBD data are derived from parental offspring information. We report on comparing IBS and IBD by applying two multiple regression models on four traits studied in the barley nested association mapping (NAM) population HEB-25. We observed that modelling parent-specific IBD genotypes produced a lower number of significant QTLs with increased prediction abilities compared with modelling IBS genotypes. However, at lower trait heritabilities the IBS model produced higher prediction abilities. We developed a method to estimate multiallelic QTL effects in multiparental populations from simple biallelic IBS data. This method is based on cumulating IBS-derived single-nucleotide polymorphism (SNP) effect estimates in a defined genetic region surrounding a QTL. Comparing the resulting parent-specific QTL effects with those obtained from IBD approaches revealed high accordance that could be confirmed through simulations. The method turned out to be also applicable to a barley multiparent advanced generation inter-cross (MAGIC) population. The 'cumulation method' represents a universal approach to differentiate parent-specific QTL effects in multiparental populations, even if no IBD information is available. In future, the method could further benefit from the availability of much denser SNP maps.

Data from: Habitat- and season-specific temperatures affect phenotypic development of hatchling lizards

Embryonic environments influence phenotypic development, but relatively few experiments have explored the effects of natural environmental variation. We incubated eggs of the lizard Anolis sagrei under conditions that mimicked natural spatial and temporal thermal variation to determine their effects on offspring morphology and performance. Incubation temperatures mimicked two microhabitats (open, shade) at two different times of the incubation season (April, July). Egg survival, incubation duration and offspring size were influenced by interactions between habitat- and season-specific nest temperatures, and locomotor performance was influenced primarily by temporal factors. These findings highlight the importance of spatial and temporal environmental variation in generating variation in fitness-related phenotypes.

opencc-zeroDec 2018View details →

Data from: Cascading reproductive isolation: plant phenology drives temporal isolation among populations of a host-specific herbivore

All organisms exist within a complex network of interacting species, thus evolutionary change may have reciprocal effects on multiple taxa. Here, we demonstrate "cascading reproductive isolation," whereby ecological differences that reduce gene flow between populations at one trophic level affect reproductive isolation (RI) among interacting species at the next trophic level. Using a combination of field, laboratory and common-garden studies and long-term herbaria records, we estimate and evaluate the relative contribution of temporal RI to overall prezygotic RI between populations of Belonocnema treatae, a specialist gall-forming wasp adapted to sister species of live oak (Quercus virginiana and Q. geminata). We link strong temporal RI between host-associated insect populations to differences between host plant budbreak phenology. Budbreak initiates flowering and the production of new leaves, which are an ephemeral resource critical to insect reproduction. As flowering time is implicated in RI between plant species, budbreak acts as a "multitrophic multi-effect trait," whereby differences in budbreak phenology contribute to RI in plants and insects. These sister oak species share a diverse community of host-specific gall-formers and insect natural enemies similarly dependent on ephemeral plant tissues. Thus, our results set the stage for testing for parallelism in a role of plant phenology in driving temporal cascading RI across multiple species and trophic levels.

opencc-zeroDec 2014View details →

Data from: Fungal specificity and selectivity for algae play a major role in determining lichen partnerships across diverse ecogeographic regions in the lichen-forming family Parmeliaceae

Microbial symbionts are instrumental to the ecological and long-term evolutionary success of their hosts, and the central role of symbiotic interactions is increasingly recognized across the vast majority of life. Lichens provide an iconic group for investigating patterns in species interactions; however, relationships among lichen symbionts are often masked by uncertain species boundaries or an inability to reliably identify symbionts. The species-rich lichen-forming fungal family Parmeliaceae provides a diverse group for assessing patterns of interactions of algal symbionts, and our study addresses patterns of lichen symbiont interactions at the largest geographic and taxonomic scales attempted to date. We analysed a total of 2356 algal internal transcribed spacer (ITS) region sequences collected from lichens representing ten mycobiont genera in Parmeliaceae, two genera in Lecanoraceae and 26 cultured Trebouxia strains. Algal ITS sequences were grouped into operational taxonomic units (OTUs); we attempted to validate the evolutionary independence of a subset of the inferred OTUs using chloroplast and mitochondrial loci. We explored the patterns of symbiont interactions in these lichens based on ecogeographic distributions and mycobiont taxonomy. We found high levels of undescribed diversity in Trebouxia, broad distributions across distinct ecoregions for many photobiont OTUs and varying levels of mycobiont selectivity and specificity towards the photobiont. Based on these results, we conclude that fungal specificity and selectivity for algal partners play a major role in determining lichen partnerships, potentially superseding ecology, at least at the ecogeographic scale investigated here. To facilitate effective communication and consistency across future studies, we propose a provisional naming system for Trebouxia photobionts and provide representative sequences for each OTU circumscribed in this study.

Data from: Mammalian herbivores affect leafhoppers associated with specific plant functional types at different timescales

1. Theory predicts that mammalian herbivores affect the quantity and quality of plants on which they preferentially feed in the short term. In the longer term, they can promote either preferred or less preferred plants, depending on whether preferred plants are adapted or sensitive to grazing. Less clear are the short- and long-term responses of herbivorous insects to mammalian herbivory, and how these responses depend on the specific plants or plant functional types on which the insects feed. 2. We progressively excluded large, medium, and small mammals for five growing seasons in two subalpine vegetation types with long-term differences in mammalian grazing intensity. Short-grass vegetation has a history of intensive grazing, while tall-grass vegetation has been grazed less intensively. We tested whether mammals altered the abundance and body size of leafhoppers specialized on specific plant functional types (grasses, sedges, forbs, or legumes/forbs), distinguishing between short-term (exclosures) and long-term (vegetation types) differences in mammalian grazing pressure. Furthermore, we assessed whether leafhoppers' responses were explained by changes in biomass or quality of the plant functional types on which they feed. 3. In the short term, mammal exclosures increased the abundance of grass- and forb-feeding leafhoppers via increases in the biomass of grasses and forbs, regardless of vegetation type. Both grasses and forbs are preferred food plants of mammals. In the long term, the biomass of sedges, which are less preferred by mammals, increased in the less intensively grazed tall-grass vegetation. This resulted in a higher abundance of sedge-feeding leafhoppers. The small size of these sedge feeders lowered the average leafhopper body size in the tall-grass vegetation. Plant nutritional quality did not explain any effects of exclusions or vegetation types. 4. Our results demonstrate that both short- and long-term effects of mammalian herbivores on the biomass of specific plant functional types caused concurrent changes in the abundance of specialized herbivorous insects, which scaled up to community-wide shifts in insect body size, a key life-history trait. A plant-functional-type approach can thus help to predict how overabundance or extinction of mammalian herbivores impacts on other components of the food web at various timescales.

Data from: The role of species-specific sensory cues in male responses to mating rivals in Drosophila melanogaster fruitflies

Complex sets of cues can be important in recognising and responding to conspecific mating competitors and avoiding potentially costly heterospecific competitive interactions. Within Drosophila. melanogaster, males can detect sensory inputs from conspecifics to assess the level of competition. They respond to rivals by significantly extending mating duration and gain significant fitness benefits from doing so. Here, we tested the idea that the multiple sensory cues used by D. melanogaster males to detect conspecifics also function to minimise 'off-target' responses to heterospecific males that they might encounter (D. simulans, D. yakuba. D. pseudoobscura or D. virilis). Focal D. melanogaster males exposed to D. simulans or D. pseudoobscura subsequently increased mating duration, but to a lesser extent than following exposure to conspecific rivals. The magnitude of rivals responses expressed by D. melanogaster males did not align with genetic distance between species and none of the sensory manipulations caused D. melanogaster to respond to males of all other species tested. However, when we removed or provided 'false' sensory cues, D. melanogaster males became more likely to show increased mating duration responses to heterospecific males. We suggest that benefits of avoiding inaccurate assessment of the competitive environment may shape the evolution of recognition cues.

Data from: Aboveground mammal and invertebrate exclusions cause consistent changes in soil food webs of two subalpine grassland types, but mechanisms are system-specific

Ungulates, smaller mammals, and invertebrates can each affect soil biota through their influence on vegetation and soil characteristics. However, direct and indirect effects of the aboveground biota on soil food webs remain to be unraveled. We assessed effects of progressively excluding aboveground large-, medium- and small-sized mammals as well as invertebrates on soil nematode diversity and feeding type abundances in two subalpine grassland types: short- and tall-grass vegetation. We explored pathways that link exclusions of aboveground biota to nematode feeding type abundances via changes in plants, soil environment, soil microbial biomass, and soil nutrients. In both vegetation types, exclusions caused a similar shift toward higher abundance of all nematode feeding types, except plant feeders, lower Shannon diversity, and lower evenness. These effects were strongest when small mammals, or both small mammals and invertebrates were excluded in addition to excluding larger mammals. Exclusions resulted in a changed abiotic soil environment that only affected nematodes in the short-grass vegetation. In each vegetation type, exclusion effects on nematode abundances were mediated by different drivers related to plant quantity and quality. In the short-grass vegetation, not all exclusion effects on omni–carnivorous nematodes were mediated by the abundance of lower trophic level nematodes, suggesting that omni–carnivores also depended on other prey than nematodes. We conclude that small aboveground herbivores have major impacts on the soil food web of subalpine short- and tall-grass ecosystems. Excluding aboveground animals caused similar shifts in soil nematode assemblages in both subalpine vegetation types, however, mechanisms turned out to be system-specific.

opencc-zeroDec 2014View details →

Data from: BrAD-seq: Breath Adapter Directional sequencing: a streamlined, ultra-simple and fast library preparation protocol for strand specific mRNA library construction

Next Generation Sequencing (NGS) is driving rapid advancement in biological understanding and RNA-sequencing (RNA-seq) has become an indispensable tool for biology and medicine. There is a growing need for access to these technologies although preparation of NGS libraries remains a bottleneck to wider adoption. Here we report a novel method for the production of strand specific RNA-seq libraries utilizing inherent properties of double-stranded cDNA to capture and incorporate a sequencing adapter. Breath Adapter Directional sequencing (BrAD-seq) reduces sample handling and requires far fewer enzymatic steps than most available methods to produce high quality strand-specific RNA-seq libraries. The method we present is optimized for 3-prime Digital Gene Expression (DGE) libraries and can easily extend to full transcript coverage shotgun (SHO) type strand-specific libraries and is modularized to accommodate a diversity of RNA and DNA input materials. BrAD-seq offers a highly streamlined and inexpensive option for RNA-seq libraries.

Data from: A single 17D Yellow Fever vaccination provides lifelong immunity; characterization of Yellow-Fever-specific neutralizing antibody and T-cell responses after vaccination

Introduction: Prompted by recent amendments of Yellow Fever (YF) vaccination guidelines from boost to single vaccination strategy and the paucity of clinical data to support this adjustment, we used the profile of the YF-specific CD8+ T-cell subset profiles after primary vaccination and neutralizing antibodies as a proxy for potentially longer lasting immunity. Methods and Findings: PBMCs and serum were collected in six individuals on days 0, 3, 5, 12, 28 and 180, and in 99 individuals >10 years after YF-vaccination. Phenotypic characteristics of YF- tetramer+ CD8+ T-cells were determined using class I tetramers. Antibody responses were measured using a standardized plaque reduction neutralization test (PRNT). Also, characteristics of YF-tetramer positive CD8+ T-cells were compared between individuals who had received a primary- and a booster vaccination. YF-tetramer+ CD8+ T-cells were detectable on day 12 (median tetramer+ cells as percentage of CD8+ T-cells 0.2%, range 0.07–3.1%). On day 180, these cells were still present (median 0.06%, range 0.02–0.78%). The phenotype of YF-tetramer positive CD8+ T-cells shifted from acute phase effector cells on day 12, to late differentiated or effector memory phenotype (CD45RA-/+CD27-) on day 28. Two subsets of YF-tetramer positive T-cells (CD45RA+CD27- and CD45RA+CD27+) persisted until day 180. Within all phenotypic subsets, the T-bet: Eomes ratio tended to be high on day 28 after vaccination and shifted towards predominant Eomes expression on day 180 (median 6.0 (day 28) vs. 2.2 (day 180) p = 0.0625), suggestive of imprinting compatible with long-lived memory properties. YF-tetramer positive CD8+ T-cells were detectable up to 18 years post vaccination, YF-specific antibodies were detectable up to 40 years after single vaccination. Booster vaccination did not increase titers of YF-specific antibodies (mean 12.5 vs. 13.1, p = 0.583), nor induce frequencies or alter phenotypes of YF-tetramer+ CD8+ T-cells. Conclusion: The presence of a functionally competent YF-specific memory T-cell pool 18 years and sufficient titers of neutralizing antibodies 35–40 years after first vaccination suggest that single vaccination may be sufficient to provide long-term immunity.

Data from: Alarm calls of a cooperative bird are referential and elicit context-specific antipredator behavior

Although functionally referential signals have been extensively studied, largely in mammals (e.g., nonhuman primates, see Cheney and Seyfarth (1988); mongooses, see Manser et al. (2002); and other ground-dwelling species, see Blumstein and Armitage (1997), other social taxa such as birds would similarly benefit from the use of referential signals. We therefore investigated alarm calling in the cooperative noisy miner (Manorina melanocephala), a species that has been anecdotally recorded producing aerial alarms to flying predators and empirically recorded generating terrestrial alarms to ground-based threats. For these signals to be truly referential however, they must meet 3 criteria. First, calls must be structurally distinct, a requirement that these 2 call types meet. Second, calls must be stimulus-specific and reliably associated with a given stimulus. We tested this on free-living birds by exposing them to a simulated aerial predator that was either in flight or subsequently perched and thus presented one of the first studies on functionally referential alarm systems where both aerial and terrestrial alarm calls have been tested. Miners only produced aerial alarms while the stimulus was in flight, switching to terrestrial alarms once it landed. Third, referential signals must elicit different escape responses that are "appropriate" to the associated threat. Under field conditions, aerial alarm playback alone provoked an almost instantaneous response of fleeing to vegetation cover, whereas terrestrial alarm playback elicited significantly slower responses by receivers and an increase in scanning behavior. During laboratory experiments, aerial alarms stimulated birds to spend more time looking upwards, whereas terrestrial alarm calls stimulated individuals to scan perpendicularly, as expected if these stimuli provided information on likely predator location. Although other avian taxa have been shown to use referential alarm signals, this system provides novel evidence of referential calls based on the behavior rather than the type of predator, providing a highly adaptive means of communicating risk to other members of the social group in this cooperative species.