Haplotype mining panel for genetic dissection and breeding in Eucalyptus.

To improve our understanding of genetic mechanisms underlying complex traits in plants, a comprehensive analysis of gene variants is required. Eucalyptus is an important forest plantation genus that is highly outbred. Trait dissection and molecular breeding in eucalypts currently relies on biallelic single-nucleotide polymorphism (SNP) markers. These markers fail to capture the large amount of haplotype diversity in these species, and thus multi-allelic markers are required. We aimed to develop a gene-based haplotype mining panel for Eucalyptus species. We generated 17 999 oligonucleotide probe sets for targeted sequencing of selected regions of 6293 genes implicated in growth and wood properties, pest and disease resistance, and abiotic stress responses. We identified and phased 195 834 SNPs using a read-based phasing approach to reveal SNP-based haplotypes. A total of 8915 target regions (at 4637 gene loci) passed tests for Mendelian inheritance. We evaluated the haplotype panel in four Eucalyptus species (E. grandis, E. urophylla, E. dunnii and E. nitens) to determine its ability to capture diversity across eucalypt species. This revealed an average of 3.13-4.52 haplotypes per target region in each species, and 33.36% of the identified haplotypes were shared by at least two species. This haplotype mining panel will enable the analysis of haplotype diversity within and between species, and provide multi-allelic markers that can be used for genome-wide association studies and gene-based breeding approaches.

Genomic consequences of artificial selection during early domestication of a wood fibre crop.

From its origins in Australia, Eucalyptus grandis has spread to every continent, except Antarctica, as a wood crop. It has been cultivated and bred for over 100 yr in places such as South Africa. Unlike most annual crops and fruit trees, domestication of E. grandis is still in its infancy, representing a unique opportunity to interrogate the genomic consequences of artificial selection early in the domestication process. To determine how a century of artificial selection has changed the genome of E. grandis, we generated single nucleotide polymorphism genotypes for 1080 individuals from three advanced South African breeding programmes using the EUChip60K chip, and investigated population structure and genome-wide differentiation patterns relative to wild progenitors. Breeding and wild populations appeared genetically distinct. We found genomic evidence of evolutionary processes known to have occurred in other plant domesticates, including interspecific introgression and intraspecific infusion from wild material. Furthermore, we found genomic regions with increased linkage disequilibrium and genetic differentiation, putatively representing early soft sweeps of selection. This is, to our knowledge, the first study of genomic signatures of domestication in a timber species looking beyond the first few generations of cultivation. Our findings highlight the importance of intra- and interspecific hybridization during early domestication.

Migrant status and identification as ultra-high risk for psychosis and transitioning to a psychotic disorder.

BACKGROUND: Certain migrant groups are more likely to develop a psychotic disorder compared to the native-born populations, and a younger age at migration is associated with greater risk. However, it is not known at which stage migration has an effect on the development of psychotic disorders. We examined whether migrants were more likely to be identified as ultra-high risk for psychosis (UHR) compared to native-born young people and whether migrant status was associated with the risk of transition to a full-threshold psychotic disorder. METHODS: The cohort included all young people aged 15-24 who were identified as UHR at a specialist clinic over a five-year period (2012-16). Australian census data were used to obtain the at-risk population. Poisson regression was used to calculate rate ratios and Cox regression analysis determined hazard ratios. RESULTS: 467 young people were identified as UHR, of which 13.5% (n = 63) were born overseas. First-generation migrants were 2.6-fold less likely to be identified as UHR compared to Australian-born young people (IRR = 0.39, 95% CI [0.30, 0.51], P < 0.001). There was no difference between migrant and native-born young people in their risk of transitioning to a psychotic disorder (HR = 0.90, 95% CI [0.39, 2.08], P = 0.81). CONCLUSIONS: UHR first-generation migrants may be under-accessing mental health services.

Asymmetries in core-collapse supernovae from maps of radioactive 44Ti in Cassiopeia A.

Asymmetry is required by most numerical simulations of stellar core-collapse explosions, but the form it takes differs significantly among models. The spatial distribution of radioactive (44)Ti, synthesized in an exploding star near the boundary between material falling back onto the collapsing core and that ejected into the surrounding medium, directly probes the explosion asymmetries. Cassiopeia A is a young, nearby, core-collapse remnant from which (44)Ti emission has previously been detected but not imaged. Asymmetries in the explosion have been indirectly inferred from a high ratio of observed (44)Ti emission to estimated (56)Ni emission, from optical light echoes, and from jet-like features seen in the X-ray and optical ejecta. Here we report spatial maps and spectral properties of the (44)Ti in Cassiopeia A. This may explain the unexpected lack of correlation between the (44)Ti and iron X-ray emission, the latter being visible only in shock-heated material. The observed spatial distribution rules out symmetric explosions even with a high level of convective mixing, as well as highly asymmetric bipolar explosions resulting from a fast-rotating progenitor. Instead, these observations provide strong evidence for the development of low-mode convective instabilities in core-collapse supernovae.

Probing human sperm metabolism using 13C-magnetic resonance spectroscopy.

STUDY QUESTION: Can 13C-Magnetic Resonance Spectroscopy (MRS) of selected metabolites provide useful information about human sperm metabolism and how glycolysis or oxidative phosphorylation are used by different sperm populations? SUMMARY ANSWER: Sperm populations, prepared by density gradient centrifugation (DGC) and incubated with either 13Cu-glucose, 13Cu-fructose or 13C1-pyruvate, showed consistent evidence of metabolism generating principally lactate and more intermittently bicarbonate, and significantly more lactate was produced from 13Cu-glucose by vital or motile sperm recovered from the 40/80% interface compared to those from the pellet, which could not be accounted for by differences in the non-sperm cells present. WHAT IS KNOWN ALREADY: Previous studies have focused on CO2 or other specific metabolite production by human sperm and there remains considerable debate about whether glycolysis and/or oxidative phosphorylation is the more important pathway for ATP production in sperm. STUDY DESIGN, SIZE, DURATION: Sperm populations were prepared by DGC and subjected to 13C-MRS to answer the following questions. (i) Is it possible to detect human sperm metabolism of 13C substrates implicated in energy generation? (ii) What are the kinetics of such reactions? (iii) Do different sperm populations (e.g. '80%' pellet sperm and '40%' interface sperm) utilise substrates in the same way? Semen samples from 97 men were used in these experiments; 52 were used in parallel for aims (i) and (ii) and 45 were used for aim (iii). PARTICIPANTS/MATERIALS, SETTING, METHODS: Sperm populations were prepared from ejaculates of healthy men using a Percoll/Phosphate Buffered Saline (PBS) DGC and then incubated with a range of 13C-labelled substrates (13Cu-glucose, 13Cu-fructose, 13C1-pyruvate, 13C1-butyrate, 13C3-lactate, 13C2,4-D-3-hydroxybutyrate, 13C5-l-glutamate, 13C1,2-glycine or 13Cu-galactose) along with penicillin/streptomycin antibiotic at 37°C for 4 h, 24 h or over 48 h for an estimated rate constant. Sperm concentration, vitality and motility were measured and, for a subset of experiments, non-sperm cell concentration was determined. A 9.4 T magnetic resonance spectrometer was used to acquire 1D 13C, inverse gated 1H decoupled, MRS spectra. Spectrum processing was carried out using spectrometer software and Matlab scripts to determine peak integrals for each spectrum. MAIN RESULTS AND THE ROLE OF CHANCE: 13Cu-glucose, 13Cu-fructose and 13C1-pyruvate were consistently converted into lactate and, to a lesser extent, bicarbonate. There was a significant correlation between sperm concentration and lactate peak size for 13Cu-glucose and 13Cu-fructose, which was not observed for 13C1-pyruvate. The lactate peak did not correlate with the non-sperm cell concentration up to 6.9 × 106/ml. The concentration of 13Cu-glucose, 13Cu-fructose or 13C1-pyruvate (1.8, 3.6, 7.2 or 14.4 mM) had no influence on the size of the observed lactate peak over a 4 h incubation. The rate of conversion of 13C1-pyruvate to lactate was approximately three times faster than for 13Cu-glucose or 13Cu-fructose which were not significantly different from each other. After incubating for 4 h, the utilisation of 13Cu-glucose, 13Cu-fructose or 13C1-pyruvate by sperm from the '40%' interface of the DGC was no different from those from the pellet when normalised to total sperm concentration. However, after normalising by either the vital or motile sperm concentration, there was a significant increase in conversion of 13Cu-glucose to lactate by '40%' interface sperm compared to pellet sperm (Vital = 3.3 ± 0.30 × 106 vs 2.0 ± 0.21 × 106; P = 0.0049; Motile = 7.0 ± 0.75 × 106 vs 4.8 ± 0.13 × 106; P = 0.0032. Mann-Whitney test P < 0.0055 taken as statistically significant). No significant differences were observed for 13Cu-fructose or 13C1-pyruvate. LARGE SCALE DATA: Not applicable. LIMITATIONS, REASONS FOR CAUTION: Only 13C labelled metabolites that accumulate to a sufficiently high concentration can be observed by 13C MRS. For this reason, intermediary molecules in the metabolic chain are difficult to observe without trapping the molecule at a particular step using inhibitors. Non-sperm cell concentration was typical of the general population and no link was found between these cells and the magnitude of the 13C-lactate peak. However, it is possible that higher concentrations than the maximum observed (6.9 × 106/ml) may contribute to exogenous substrate metabolism in other experiments. WIDER IMPLICATIONS OF THE FINDINGS: 13C-MRS can provide information on the underlying metabolism of multiple pathways in live sperm. Dysfunction in sperm metabolism, as a result of either impaired enzymes of lack of metabolisable substrate, could be detected in sperm by a non-destructive assay, potentially offering new treatment options to improve overall sperm quality and outcomes for reproduction. STUDY FUNDING AND COMPETING INTERESTS: This work was supported by the Medical Research Council Grant MR/M010473/1. The authors declare no conflicts of interest.

Long-term dietary shift and population decline of a pelagic seabird-A health check on the tropical Atlantic?

In the face of accelerating ecological change to the world's oceans, seabirds are some of the best bio-indicators of marine ecosystem function. However, unravelling ecological changes that pre-date modern monitoring programmes remains challenging. Using stable isotope analysis of feathers and regurgitants collected from sooty terns (Onychoprion fuscatus) nesting at a major Atlantic colony, we reconstructed a long-term dietary time series from 1890 to the present day and show that a significant dietary shift occurred during the second half of the twentieth century coinciding with an apparent population collapse of approximately 84%. After correcting for the "Suess Effect," δ13 C in feathers declined by ~1.5‰ and δ15 N by ~2‰ between the 1890s and the present day, indicating that birds changed their diets markedly over the period of population decline. Isotopic niches were equally wide before and after the population collapse but isotopic mixing models suggest that birds have grown ever more reliant on nutrient-poor squid and invertebrates as teleost fish have declined in availability. Given that sooty terns rely heavily on associations with sub-surface predators such as tuna to catch fish prey, the rapid expansion of industrialized fisheries for these species over the same period seems a plausible mechanism. Our results suggest that changes to marine ecosystems over the past 60 years have had a dramatic impact on the ecology of the most abundant seabird of tropical oceans, and highlight the potentially pervasive consequences of large predatory fish depletion on marine ecosystem function.

Associations between Escherichia coli O157 shedding and the faecal microbiota of dairy cows.

AIMS: Dairy cattle shed pathogenic Escherichia coli O157 (O157) in faeces, playing a role in human exposure. We aimed to measure faecal microbial communities in early lactation dairy cattle, and model outcomes with O157 shedding metrics. METHODS AND RESULTS: Daily faecal samples were collected from 40 cattle on two Colorado dairies for five consecutive days, and characterized for O157. 16S rRNA gene sequencing was used to measure sample-level microbial communities. Alpha-diversity metrics were associated with O157 outcomes via regression modelling, adjusting for confounders. Differential abundance of taxa were identified between O157(+) and O157(-) samples and between shedding days of individuals, using matched Wilcoxon rank-sum tests, zero-inflated Gaussian (ZIG) regression and negative binomial regression. After removing an outlier, multi-day and intermittently shedding cows had lower average richness compared to those that never shed. ZIG modelling revealed Bacillus coagulans to be more abundant in O157(-) samples, while Moryella were more abundant in O157(+) samples. Negative binomial models and Wilcoxon tests revealed no differentially abundant taxa between O157(+) vs O157(-) samples, or between shedding days of individuals. CONCLUSIONS: Microbial diversity and some taxa may be influenced by or affect O157 shedding by dairy cattle. SIGNIFICANCE AND IMPACT OF THE STUDY: If future work corroborates these findings, dairy cow microbial community changes may be used to guide on-farm strategies that mitigate O157 dissemination, protecting the human food chain.

Exposure to household air pollution from biomass-burning cookstoves and HbA1c and diabetic status among Honduran women.

Household air pollution from biomass cookstoves is estimated to be responsible for more than two and a half million premature deaths annually, primarily in low and middle-income countries where cardiometabolic disorders, such as Type II Diabetes, are increasing. Growing evidence supports a link between ambient air pollution and diabetes, but evidence for household air pollution is limited. This cross-sectional study of 142 women (72 with traditional stoves and 70 with cleaner-burning Justa stoves) in rural Honduras evaluated the association of exposure to household air pollution (stove type, 24-hour average kitchen and personal fine particulate matter [PM2.5 ] mass and black carbon) with glycated hemoglobin (HbA1c) levels and diabetic status based on HbA1c levels. The prevalence ratio (PR) per interquartile range increase in pollution concentration indicated higher prevalence of prediabetes/diabetes (vs normal HbA1c) for all pollutant measures (eg, PR per 84 µg/m3 increase in personal PM2.5 , 1.49; 95% confidence interval [CI], 1.11-2.01). Results for HbA1c as a continuous variable were generally in the hypothesized direction. These results provide some evidence linking household air pollution with the prevalence of prediabetes/diabetes, and, if confirmed, suggest that the global public health impact of household air pollution may be broader than currently estimated.

Lost in plasmids: next generation sequencing and the complex genome of the tick-borne pathogen Borrelia burgdorferi.

BACKGROUND: Borrelia (B.) burgdorferi sensu lato, including the tick-transmitted agents of human Lyme borreliosis, have particularly complex genomes, consisting of a linear main chromosome and numerous linear and circular plasmids. The number and structure of plasmids is variable even in strains within a single genospecies. Genes on these plasmids are known to play essential roles in virulence and pathogenicity as well as host and vector associations. For this reason, it is essential to explore methods for rapid and reliable characterisation of molecular level changes on plasmids. In this study we used three strains: a low passage isolate of B. burgdorferi sensu stricto strain B31(-NRZ) and two closely related strains (PAli and PAbe) that were isolated from human patients. Sequences of these strains were compared to the previously sequenced reference strain B31 (available in GenBank) to obtain proof-of-principle information on the suitability of next generation sequencing (NGS) library construction and sequencing methods on the assembly of bacterial plasmids. We tested the effectiveness of different short read assemblers on Illumina sequences, and of long read generation methods on sequence data from Pacific Bioscience single-molecule real-time (SMRT) and nanopore (Oxford Nanopore Technologies) sequencing technology. RESULTS: Inclusion of mate pair library reads improved the assembly in some plasmids as did prior enrichment of plasmids. While cp32 plasmids remained refractory to assembly using only short reads they were effectively assembled by long read sequencing methods. The long read SMRT and nanopore sequences came, however, at the cost of indels (insertions or deletions) appearing in an unpredictable manner. Using long and short read technologies together allowed us to show that the three B. burgdorferi s.s. strains investigated here, whilst having similar plasmid structures to each other (apart from fusion of cp32 plasmids), differed significantly from the reference strain B31-GB, especially in the case of cp32 plasmids. CONCLUSION: Short read methods are sufficient to assemble the main chromosome and many of the plasmids in B. burgdorferi. However, a combination of short and long read sequencing methods is essential for proper assembly of all plasmids including cp32 and thus, for gaining an understanding of host- or vector adaptations. An important conclusion from our work is that the evolution of Borrelia plasmids appears to be dynamic. This has important implications for the development of useful research strategies to monitor the risk of Lyme disease occurrence and how to medically manage it.

1H Magnetic Resonance Spectroscopy of live human sperm.

STUDY QUESTION: Can 1H Magnetic Resonance Spectroscopy (MRS) be used to obtain information about the molecules and metabolites in live human spermatozoa? SUMMARY ANSWER: Percoll-based density gradient centrifugation (DGC) followed by a further two washing steps, yielded enough sperm with minimal contamination (<0.01%) from seminal fluid to permit effective MRS which detected significant differences (P < 0.05) in the choline/glycerophosphocholine (GPC), lipid and lactate regions of the 1H MRS spectrum between sperm in the pellet and those from the 40%/80% interface. WHAT IS KNOWN ALREADY: Current methods to examine sperm are either limited in their value (e.g. semen analysis) or are destructive (e.g. immunohistochemistry, sperm DNA testing). A few studies have previously used MRS to examine sperm, but these have either looked at seminal plasma from men with different ejaculate qualities or at the molecules present in pooled samples of lyophilized sperm. STUDY DESIGN, SAMPLES/MATERIALS, METHODS: Sperm suspended in phosphate buffered saline (PBS) at 37°C were examined by 1H MRS scanning using a 1H excitation-sculpting solvent suppression sequence after recovery from fresh ejaculates by one of three different methods: (i) simple centrifugation; (ii) DGC with one wash; or (iii) DGC with two washes. In the case of DGC, sperm were collected both from the pellet ('80%' sperm) and the 40/80 interface ('40%' sperm). Spectrum processing was carried out using custom Matlab scripts to determine; the degree of seminal plasma/Percoll contamination, the minimum sperm concentration for 1H MRS detection and differences between the 1H MRS spectra of '40%' and '80%' sperm. MAIN RESULTS AND THE ROLE OF CHANCE: DGC with two washes minimized the 1H MRS peak intensity for both seminal plasma and Percoll/PBS solution contamination while retaining sperm specific peaks. For the MRS scanner used in this study, the minimum sperm concentration required to produce a choline/GPC 1H MRS peak greater than 3:1 signal to noise ratio (SNR) was estimated at ~3 × 106/ml. The choline/GPC and lactate/lipid regions of the 1H spectrum were significantly different by two-way ANOVA analysis (P < 0.0001; n = 20). ROC curve analysis of these region showed significant ability to distinguish between the two sperm populations: choline/GPC ROC AUC = 0.65-0.67, lactate/lipid ROC AUC = 0.86-0.87. LIMITATIONS, REASONS FOR CAUTION: Only 3-4 semen samples were used to assess the efficacy of each sperm washing protocol that were examined. The estimated minimum sperm concentration required for MRS is specific to the hardware used in our study and may be different in other spectrometers. Spectrum binning is a low resolution analysis method that sums MRS peaks within a chemical shift range. This can obscure the identity of which metabolite(s) are responsible for differences between sperm populations. Further work is required to determine the relative contribution of somatic cells to the MRS spectrum from the '40%' and '80%' sperm. WIDER IMPLICATIONS OF THE FINDINGS: 1H MRS can provide information about the molecules present in live human sperm and may therefore permit the study of the underlying functional biology or metabolomics of live sperm. Given the relatively low concentration of sperm required to obtain a suitable MRS signal (~3 × 106/ml), this could be carried out on sperm from men with oligo-, astheno- or teratozoospermia. This may lead to the development of new diagnostic tests or ultimately novel treatments for male factor infertility. STUDY FUNDING AND COMPETING INTEREST(S): This work was supported by the Medical Research Council Grant MR/M010473/1. The authors declare no conflicts of interest.

Do they stay or do they go? Acoustic monitoring of whale sharks at Ningaloo Marine Park, Western Australia.

Whale sharks Rhincodon typus were monitored via acoustic transmitters at the northern end of Western Australia's Ningaloo Marine Park to establish the extent to which the species inhabits the region beyond the whale-shark ecotourism industry season, which usually extends from March to August in each year. Despite the vast majority (c. 98%) of photographic submissions of R. typus from Ningaloo Reef being between March and August, acoustic detections from the tagged R. typus at Ningaloo were recorded in all months of the year, but do not preclude the occurrence of extended absences. It is concluded that as a species, R. typus occurs year round at Ningaloo, where it generally remains in close proximity to the reef edge, but that some individuals move outside of the detection range of the array for extended periods.

CRISPR-Cas9-mediated gene knockout in primary human airway epithelial cells reveals a proinflammatory role for MUC18.

Targeted knockout of genes in primary human cells using CRISPR-Cas9-mediated genome-editing represents a powerful approach to study gene function and to discern molecular mechanisms underlying complex human diseases. We used lentiviral delivery of CRISPR-Cas9 machinery and conditional reprogramming culture methods to knockout the MUC18 gene in human primary nasal airway epithelial cells (AECs). Massively parallel sequencing technology was used to confirm that the genome of essentially all cells in the edited AEC populations contained coding region insertions and deletions (indels). Correspondingly, we found mRNA expression of MUC18 was greatly reduced and protein expression was absent. Characterization of MUC18 knockout cell populations stimulated with TLR2, 3 and 4 agonists revealed that IL-8 (a proinflammatory chemokine) responses of AECs were greatly reduced in the absence of functional MUC18 protein. Our results show the feasibility of CRISPR-Cas9-mediated gene knockouts in AEC culture (both submerged and polarized), and suggest a proinflammatory role for MUC18 in airway epithelial response to bacterial and viral stimuli.

Parasitic scabies mites and associated bacteria joining forces against host complement defence.

Scabies is a ubiquitous and contagious skin disease caused by the parasitic mite Sarcoptes scabiei Epidemiological studies have identified scabies as a causative agent for secondary skin infections caused by Staphylococcus aureus and Streptococcus pyogenes. This is an important notion, as such bacterial infections can lead to serious downstream life-threatening complications. As the complement system is the first line of host defence that confronts invading pathogens, both the mite and bacteria produce a large array of molecules that inhibit the complement cascades. It is hypothesised that scabies mite complement inhibitors may play an important role in providing a favourable micro-environment for the establishment of secondary bacterial infections. This review aims to bring together the current literature on complement inhibition by scabies mites and bacteria associated with scabies and to discuss the proposed molecular link between scabies and bacterial co-infections.

Birds as bioindicators of plastic pollution in terrestrial and freshwater environments: A 30-year review.

Plastic pollution is a global concern that has grown ever more acute in recent years. Most research has focused on the impact of plastic pollution in marine environments. However, plastic is increasingly being detected in terrestrial and freshwater environments with key inland sources including landfills, where it is accessible to a wide range of organisms. Birds are effective bioindicators of pollutants for many reasons, including their high mobility and high intra- and interspecific variation in trophic levels. Freshwater and terrestrial bird species are under-represented in plastic pollution research compared to marine species. We reviewed 106 studies (spanning from 1994 onwards) that have detected plastics in bird species dwelling in freshwater and/or terrestrial habitats, identifying knowledge gaps. Seventy-two studies focused solely on macroplastics (fragments >5 mm), compared to 22 microplastic (fragments <5 mm) studies. A further 12 studies identified plastics as both microplastics and macroplastics. No study investigated nanoplastic (particles <100 nm) exposure. Research to date has geographical and species' biases while ignoring nanoplastic sequestration in free-living freshwater, terrestrial and marine bird species. Building on the baseline search presented here, we urge researchers to develop and validate standardised field sampling techniques and laboratory analytical protocols such as Raman spectroscopy to allow for the quantification and identification of micro- and nanoplastics in terrestrial and freshwater environments and the species therein. Future studies should consistently report the internalised and background concentrations, types, sizes and forms of plastics. This will enable a better understanding of the sources of plastic pollution and their routes of exposure to birds of terrestrial and freshwater environments, providing a more comprehensive insight into the potential impacts on birds.

Kinetic modeling of hyperpolarized (13)C pyruvate metabolism in tumors using a measured arterial input function.

Mathematical models are required to estimate kinetic parameters of [1-(13)C] pyruvate-lactate interconversion from magnetic resonance spectroscopy data. One- or two-way exchange models utilizing a hypothetical approximation to the true arterial input function (AIF), (e.g. an ideal 'box-car' function) have been used previously. We present a method for direct measurement of the AIF in the rat. The hyperpolarized [1-(13)C] pyruvate signal was measured in arterial blood as it was continuously withdrawn through a small chamber. The measured signal was corrected for T1 relaxation of pyruvate, RF pulses and dispersion of blood in the chamber to allow for the estimation of the direct AIF. Using direct AIF, rather than the commonly used box-car AIF, provided realistic estimates of the rate constant of conversion of pyruvate to lactate, kpl, the rate constant of conversion of lactate to pyruvate klp, the clearance rate constant of pyruvate from blood to tissue, Kip, and the relaxation rate of lactate T1la. Since no lactate signal was present in blood, it was possible to use a simple precursor-product relationship, with the tumor tissue pyruvate time-course as the input for the lactate time-course. This provided a robust estimate of kpl, similar to that obtained using a directly measured AIF.

Condition-dependent strategies of eggshell pigmentation: an experimental study of Japanese quail (Coturnix coturnix japonica).

A relationship has been suggested between eggshell colour and female body condition based on the opposing antioxidant properties of the two main eggshell pigments: the antioxidant biliverdin (blue-green) and the pro-oxidant protoporphyrin (brown). We hypothesized that experimentally food-restricted females with low antioxidant capacity would deposit more protoporphyrin and less biliverdin in their eggshells, resulting in eggshells of reduced brightness but increased colour intensity. Two eggs were collected at the beginning and two at the end of a 2 week period from each of 24 female Japanese quails that were either food restricted or receiving ad libitum food (i.e. controls) during that time. Reflectance spectra were recorded and analysed using spectral shape descriptors, chromatic and achromatic contrasts were computed accounting for avian visual sensitivities, and eggshell pigments were quantified. We examined both spot and background pigmentation and found no significant effect of food restriction on eggshell reflectance. However, food-restricted females in lower body condition increased the deposition of protoporphyrin and decreased the amount of biliverdin invested in their eggshells. We hypothesize that in species laying brown-spotted eggshells, females modulate eggshell pigment investment in response to their body condition. According to this hypothesis, we predict that females maintain eggshell colour to limit visible changes that could be detected by predators and thereby conceal their eggs, although this work has yet to be conducted. We suggest that further experimental work on egg camouflage under different environmental conditions will elaborate on the process of pigment deposition and the physiological costs to females of laying heavily pigmented eggshells.

Impact of a cleaner-burning cookstove intervention on blood pressure in Nicaraguan women.

Few studies have evaluated the cardiovascular-related effects of indoor biomass burning or the role of characteristics such as age and obesity status, in this relationship. We examined the impact of a cleaner-burning cookstove intervention on blood pressure among Nicaraguan women using an open fire at baseline; we also evaluated heterogeneity of the impact by subgroups of the population. We evaluated changes in systolic and diastolic blood pressure from baseline to post-intervention (range: 273-383 days) among 74 female cooks. We measured indoor fine particulate matter (PM(2.5); N = 25), indoor carbon monoxide (CO; N = 32), and personal CO (N = 30) concentrations. Large mean reductions in pollutant concentrations were observed for all pollutants; for example, indoor PM(2.5) was reduced 77% following the intervention. However, pollution distributions (baseline and post-intervention) were wide and overlapping. Although substantial reductions in blood pressure were not observed among the entire population, a 5.9 mmHg reduction [95% confidence interval (CI): -11.3, -0.4] in systolic blood pressure was observed among women aged 40 or more years and a 4.6 mmHg reduction (95% CI: -10.0, 0.8) was observed among obese women. Results from this study provide an indication that certain subgroups may be more likely to experience improvements in blood pressure following a cookstove intervention.

Why do some bird species incorporate more anthropogenic materials into their nests than others?

Many bird species incorporate anthropogenic materials (e.g. sweet wrappers, cigarette butts and plastic strings) into their nests. Anthropogenic materials have become widely available as nesting materials in marine and terrestrial environments globally. These human-made objects can provide important benefits to birds such as serving as reliable signals to conspecifics or protecting against ectoparasites, but they can also incur fundamental survival and energetic costs via offspring entanglement and reduced insulative properties, respectively. From an ecological perspective, several hypotheses have been proposed to explain the use of anthropogenic nest materials (ANMs) by birds but no previous interspecific study has tried to identify the underlying mechanisms of this behaviour. In this study, we performed a systematic literature search and ran phylogenetically controlled comparative analyses to examine interspecific variation in the use of ANM and to examine the influence of several ecological and life-history traits. We found that sexual dimorphism and nest type significantly influenced the use of ANMs by birds providing support for the 'signalling hypothesis' that implies that ANMs reflect the quality of the nest builder. However, we found no support for the 'age' and 'new location' hypotheses, nor for a phylogenetic pattern in this behaviour, suggesting that it is widespread throughout birds. This article is part of the theme issue 'The evolutionary ecology of nests: a cross-taxon approach'.