Lytic to temperate switching of viral communities.

Microbial viruses can control host abundances via density-dependent lytic predator-prey dynamics. Less clear is how temperate viruses, which coexist and replicate with their host, influence microbial communities. Here we show that virus-like particles are relatively less abundant at high host densities. This suggests suppressed lysis where established models predict lytic dynamics are favoured. Meta-analysis of published viral and microbial densities showed that this trend was widespread in diverse ecosystems ranging from soil to freshwater to human lungs. Experimental manipulations showed viral densities more consistent with temperate than lytic life cycles at increasing microbial abundance. An analysis of 24 coral reef viromes showed a relative increase in the abundance of hallmark genes encoded by temperate viruses with increased microbial abundance. Based on these four lines of evidence, we propose the Piggyback-the-Winner model wherein temperate dynamics become increasingly important in ecosystems with high microbial densities; thus 'more microbes, fewer viruses'.

Mussismilia braziliensis White Plague Disease Is Characterized by an Affected Coral Immune System and Dysbiosis.

Infectious diseases are one of the major drivers of coral reef decline worldwide. White plague-like disease (WPL) is a widespread disease with a complex etiology that infects several coral species, including the Brazilian endemic species Mussismilia braziliensis. Gene expression profiles of healthy and WPL-affected M. braziliensis were analyzed in winter and summer seasons. The de novo assembly of the M. braziliensis transcriptome from healthy and white plague samples produced a reference transcriptome containing 119,088 transcripts. WPL-diseased samples were characterized by repression of immune system and cellular defense processes. Autophagy and cellular adhesion transcripts were also repressed in WPL samples, suggesting exhaustion of the coral host defenses. Seasonal variation leads to plasticity in transcription with upregulation of intracellular signal transduction, apoptosis regulation, and oocyte development in the summer. Analysis of the active bacterial rRNA indicated that Pantoea bacteria were more abundant in WPL corals, while Tistlia, Fulvivirga, and Gammaproteobacteria Ga0077536 were more abundant in healthy samples. Cyanobacteria proliferation was also observed in WPL, mostly in the winter. These results indicate a scenario of dysbiosis in WPL-affected M. braziliensis, with the loss of potentially symbiotic bacteria and proliferation of opportunistic microbes after the start of the infection process.

Spontaneous abortion as a response to reproductive conflict in the banded mongoose.

When breeding females compete for limited resources, the intensity of this reproductive conflict can determine whether the fitness benefits of current reproductive effort exceed the potential costs to survival and future fertility. In group-living species, reproductive competition can occur through post-natal competition among the offspring of co-breeding females. Spontaneous abortion could be a response to such competition, allowing females to curtail reproductive expenditure on offspring that are unlikely to survive and to conserve resources for future breeding opportunities. We tested this hypothesis using long-term data on banded mongooses, Mungos mungo, in which multiple females within a group give birth synchronously to a communal litter that is cared for by other group members. As predicted, abortions were more likely during dry periods when food is scarce, and in breeding attempts with more intense reproductive competition. Within breeding events, younger, lighter females carrying smaller fetuses were more likely to abort, particularly those that were also of lower rank. Our results suggest that abortion may be a means by which disadvantaged females conserve resources for future breeding attempts in more benign conditions, and highlight that female reproductive competition may be resolved long before the production of offspring.

Proposal of fifteen new species of Parasynechococcus based on genomic, physiological and ecological features.

Members of the recently proposed genus Parasynechococcus (Cyanobacteria) are extremely abundant throughout the global ocean and contribute significantly to global primary productivity. However, the taxonomy of these organisms remains poorly characterized. The aim of this study was to propose a new taxonomic framework for Parasynechococcus based on a genomic taxonomy approach that incorporates genomic, physiological and ecological data. Through in silico DNA-DNA hybridization, average amino acid identity, dinucleotide signatures and phylogenetic reconstruction, a total of 15 species of Parasynechococcus could be delineated. Each species was then described on the basis of their gene content, light and nutrient utilization strategies, geographical distribution patterns throughout the oceans and response to environmental parameters.

Trends in Indigenous and non-Indigenous caesarean section births in the Northern Territory of Australia, 1986-2012: a total population-based study.

OBJECTIVE: To examine trends in caesarean section deliveries and factors associated with these trends for Indigenous and non-Indigenous mothers. DESIGN: Total population-based study. SETTING: Northern Territory of Australia, 1986-2012. POPULATION: Pregnancies among Northern Territory residents, limited to singleton live births with cephalic presentations delivered at 37-42 weeks' gestation (n = 78 561). METHODS: Descriptive analyses of demographic and obstetric risk factors. Poisson regression with robust variance to estimate the likelihood of caesarean delivery with and without labour compared with vaginal delivery, over time and between Indigenous and non-Indigenous mothers, adjusting for risk factors. MAIN OUTCOME MEASURES: Trends in caesarean sections and risk of caesarean delivery compared with vaginal delivery. RESULTS: The total rate of caesarean deliveries in the Northern Territory increased between 1986 and 2012. From the year 2000, the rise was driven by increases in caesareans with labour among nulliparous mothers and no labour caesareans among multiparous mothers. Increases in demographic and obstetric risk factors explained the rise in caesareans with labour among nulliparous Indigenous mothers, whereas other unmeasured variables contributed to the rise among non-Indigenous mothers. Increases in previous caesarean delivery contributed to the rise in all caesareans among multiparous mothers. Following adjustment, the risk of Indigenous nulliparous mothers having a caesarean with labour was 47% greater than for non-Indigenous nulliparous mothers [adjusted risk ratio 1.47 (95% CI 1.34-1.60)]. CONCLUSIONS: Increases in demographic and obstetric risk factors partially explained the increase in caesarean rates in the Northern Territory and the contribution of these factors differed between Indigenous and non-Indigenous mothers. TWEETABLE ABSTRACT: Caesarean section rates increased between 1986 and 2012 in the Northern Territory of Australia.

FRAX-based assessment and intervention thresholds--an exploration of thresholds in women aged 50 years and older in the UK.

UNLABELLED: Under current guidelines, based on prior fracture probability thresholds, inequalities in access to therapy arise especially at older ages (≥70 years) depending on the presence or absence of a prior fracture. An alternative threshold (a fixed threshold from the age of 70 years) reduces this disparity, increases treatment access and decreases the need for bone densitometry. INTRODUCTION: Several international guidelines set age-specific intervention thresholds at the 10-year probability of fracture equivalent to a woman of average BMI with a prior fracture. At older ages (≥70 years), women with prior fracture selected for treatment are at lower average absolute risk than those selected for treatment in the absence of prior fracture, prompting consideration of alternative thresholds in this age group. METHODS: Using a simulated population of 50,633 women aged 50-90 years in the UK, with a distribution of risk factors similar to that in the European FRAX derivation cohorts and a UK-matched age distribution, the current NOGG intervention and assessment thresholds were compared to one where the thresholds remained constant from 70 years upwards. RESULTS: Under current thresholds, 45.1% of women aged ≥70 years would be eligible for therapy, comprising 37.5% with prior fracture, 2.2% with high risk but no prior fracture and 5.4% selected for treatment after bone mineral density (BMD) measurement. Mean hip fracture probability was 11.3, 23.3 and 17.6%, respectively, in these groups. Under the alternative thresholds, the overall proportion of women treated increased from 45.1 to 52.9%, with 8.4% at high risk but no prior fracture and 7.0% selected for treatment after BMD measurement. In the latter group, the mean probability of hip fracture was identical to that observed in women with prior fracture (11.3%). The alternative threshold also reduced the need for BMD measurement, particularly at older ages (>80 years). CONCLUSIONS: The alternative thresholds equilibrate fracture risk, particularly hip fracture risk, in those with or without prior fracture selected for treatment and reduce BMD usage at older ages.

Elevated glucocorticoid concentrations during gestation predict reduced reproductive success in subordinate female banded mongooses.

Dominant females in social species have been hypothesized to reduce the reproductive success of their subordinates by inducing elevated circulating glucocorticoid (GC) concentrations. However, this 'stress-related suppression' hypothesis has received little support in cooperatively breeding species, despite evident reproductive skews among females. We tested this hypothesis in the banded mongoose (Mungos mungo), a cooperative mammal in which multiple females conceive and carry to term in each communal breeding attempt. As predicted, lower ranked females had lower reproductive success, even among females that carried to term. While there were no rank-related differences in faecal glucocorticoid (fGC) concentrations prior to gestation or in the first trimester, lower ranked females had significantly higher fGC concentrations than higher ranked females in the second and third trimesters. Finally, females with higher fGC concentrations during the third trimester lost a greater proportion of their gestated young prior to their emergence from the burrow. Together, our results are consistent with a role for rank-related maternal stress in generating reproductive skew among females in this cooperative breeder. While studies of reproductive skew frequently consider the possibility that rank-related stress reduces the conception rates of subordinates, our findings highlight the possibility of detrimental effects on reproductive outcomes even after pregnancies have become established.

3D printed metal columns for capillary liquid chromatography.

Coiled planar capillary chromatography columns (0.9 mm I.D. × 60 cm L) were 3D printed in stainless steel (316L), and titanium (Ti-6Al-4V) alloys (external dimensions of ~5 × 30 × 58 mm), and either slurry packed with various sized reversed-phase octadecylsilica particles, or filled with an in situ prepared methacrylate based monolith. Coiled printed columns were coupled directly with 30 × 30 mm Peltier thermoelectric direct contact heater/cooler modules. Preliminary results show the potential of using such 3D printed columns in future portable chromatographic devices.

Bone loss in a new rodent model combining spinal cord injury and cast immobilization.

OBJECTIVES: Characterize bone loss in our newly developed severe contusion spinal cord injury (SCI) plus hindlimb immobilization (IMM) model and determine the influence of muscle contractility on skeletal integrity after SCI. METHODS: Female Sprague-Dawley rats were randomized to: (a) intact controls, (b) severe contusion SCI euthanized at Day 7 (SCI-7) or (c) Day 21 (SCI-21), (d) 14 days IMM-alone, (e) SCI+IMM, or (f) SCI+IMM plus 14 days body weight supported treadmill exercise (SCI+IMM+TM). RESULTS: SCI-7 and SCI-21 exhibited a >20% reduction in cancellous volumetric bone mineral density (vBMD) in the hindlimbs (p⋜0.01), characterized by reductions in cancellous bone volume (cBV/TV%), trabecular number (Tb.N), and trabecular thickness. IMM-alone induced no observable bone loss. SCI+IMM exacerbated cancellous vBMD deficits with values being >45% below Controls (p⋜0.01) resulting from reduced cBV/TV% and Tb.N. SCI+IMM also produced the greatest cortical bone loss with distal femoral cortical area and cortical thickness being 14-28% below Controls (p⋜0.01) and bone strength being 37% below Controls (p⋜0.01). SCI+IMM+TM partially alleviated bone deficits, but values remained below Controls. CONCLUSIONS: Residual and/or facilitated muscle contractility ameliorate bone decrements after severe SCI. Our novel SCI+IMM model represents a clinically-relevant means of assessing strategies to prevent SCI-induced skeletal deficits.

Episodic radiations in the fly tree of life.

Flies are one of four superradiations of insects (along with beetles, wasps, and moths) that account for the majority of animal life on Earth. Diptera includes species known for their ubiquity (Musca domestica house fly), their role as pests (Anopheles gambiae malaria mosquito), and their value as model organisms across the biological sciences (Drosophila melanogaster). A resolved phylogeny for flies provides a framework for genomic, developmental, and evolutionary studies by facilitating comparisons across model organisms, yet recent research has suggested that fly relationships have been obscured by multiple episodes of rapid diversification. We provide a phylogenomic estimate of fly relationships based on molecules and morphology from 149 of 157 families, including 30 kb from 14 nuclear loci and complete mitochondrial genomes combined with 371 morphological characters. Multiple analyses show support for traditional groups (Brachycera, Cyclorrhapha, and Schizophora) and corroborate contentious findings, such as the anomalous Deuterophlebiidae as the sister group to all remaining Diptera. Our findings reveal that the closest relatives of the Drosophilidae are highly modified parasites (including the wingless Braulidae) of bees and other insects. Furthermore, we use micro-RNAs to resolve a node with implications for the evolution of embryonic development in Diptera. We demonstrate that flies experienced three episodes of rapid radiation--lower Diptera (220 Ma), lower Brachycera (180 Ma), and Schizophora (65 Ma)--and a number of life history transitions to hematophagy, phytophagy, and parasitism in the history of fly evolution over 260 million y.

Nosocomial outbreak of staphyloccocal scalded skin syndrome in neonates in England, December 2012 to March 2013.

Staphylococcal scalded skin syndrome (SSSS) is a blistering skin condition caused by exfoliative toxin-producing strains of Staphylococcus aureus. Outbreaks of SSSS in maternity settings are rarely reported. We describe an outbreak of SSSS that occurred among neonates born at a maternity unit in England during December 2012 to March 2013. Detailed epidemiological and microbiological investigations were undertaken. Eight neonates were found to be infected with the outbreak strain of S. aureus, of spa type t346, representing a single pulsotype. All eight isolates contained genes encoding exfoliative toxin A (eta) and six of them contained genes encoding toxin B (etb). Nasal swabs taken during targeted staff screening yielded a staphylococcal carriage rate of 21% (17/80), but none contained the outbreak strain. Mass screening involving multi-site swabbing and pooled, enrichment culture identified a healthcare worker (HCW) with the outbreak strain. This HCW was known to have a chronic skin condition and their initial nasal screen was negative. The outbreak ended when they were excluded from work. This outbreak highlights the need for implementing robust swabbing and culture methodswhen conventional techniques are unsuccessful in identifying staff carrier(s). This study adds to the growing body of evidence on the role of HCWs in nosocomial transmission of S. aureus.

Genomic and physiological characterization of Kitasatospora sp. nov., an actinobacterium with potential for biotechnological application isolated from Cerrado soil.

An Actinobacteria - Kitasatospora sp. K002 - was isolated from the soil of Cerrado, a savanna-like Brazilian biome. Herein, we conducted a phylogenetic, phenotypic and physiological characterization, revealing its potential for biotechnological applications. Kitasatospora sp. K002 is an aerobic, non-motile, Gram-positive bacteria that forms grayish-white mycelium on solid cultures and submerged spores with vegetative mycelia on liquid cultures. The strain showed antibacterial activity against Bacillus subtilis, Pseudomonas aeruginosa and Escherichia coli. Genomic analysis indicated that Kitasatospora xanthocidica JCM 4862 is the closest strain to K002, with a dDDH of 32.8-37.8% and an ANI of 86.86% and the pangenome investigations identified a high number of rare genes. A total of 60 gene clusters of 22 different types were detected by AntiSMASH, and 22 gene clusters showed low similarity (< 10%) with known compounds, which suggests the potential production of novel bioactive compounds. In addition, phylogenetic analysis and morphophysiological characterization clearly distinguished Kitasatospora sp. K002 from other related species. Therefore, we propose that Kitasatospora sp. K002 should be recognized as a new species of the genus Kitasatospora - Kitasatospora brasiliensis sp. nov. (type strains = K002).

Seasonal and diel modulation of DOM in a mangrove-dominated estuary.

Rivers and estuaries are the main links between continents and oceans. The Paraíba do Sul River is among the most important rivers of the southeastern Brazilian region, carrying an average of 0.08 Tg of dissolved organic matter (DOM) to the ocean but has been facing significant changes in river discharge. In this study, we aimed to provide insights into the sources and transformations of chromophoric dissolved organic matter (CDOM) and fluorescent dissolved organic matter (FDOM) sources across a salinity gradient under changing river discharge scenarios. Three spatial surveys were performed covering the entire salinity gradient of the main estuarine channel and surrounding mangrove waters under contrasting river discharge (178 to 1240 m3 s-1), and diel sampling was conducted in the mangrove tidal creek. The characterization of DOM through the parallel factor analysis (PARAFAC) model identified six components across the river-ocean gradient and mangrove creek: terrestrial origin (C1 - fulvic acid and C2 and C3 - humic-like), protein-like (C4), tryptophan-like (C5), and tyrosine-like (C6). Our results showed a shift in DOM composition and contribution along the salinity gradient, from terrestrial (C3) to autochthonous (C5 and C6) signatures. The October-17 dry campaign was characterized by a higher proportion of microbial protein-like component C4 and a lower contribution of humic-like components compared to February-17 and March-18 across the salinity gradient with an increase in the mixing zone. The DOM compositions of the February 17 dry and March 18 wet campaigns were similar. Additionally, the March-18 wet campaign, marked by the highest river discharge, showed higher inputs of terrestrial DOM (C1-C3 components) compared to February-17 in the estuary, which allowed DOM to be transported rather than transformed. The mangrove diel study showed that tidal fluctuations are also an important driver of carbon input to the mangrove creek with a possible impact on DOM composition in estuarine waters.

Caregiver's cognitive traits are associated with pup fitness in a cooperatively breeding mammal.

Studies across diverse taxa have revealed the importance of early life environment and parenting on characteristics later in life. While some have shown how early life experiences can impact cognitive abilities, very few have turned this around and looked at how the cognitive skills of parents or other carers during early life affect the fitness of young. In this study, we investigate how the characteristics of carers may affect proxies of fitness of pups in the cooperatively breeding banded mongoose (Mungos mungo). We gave adult mongooses a spatial memory test and compared the results to the success of the pups those individuals cared for. Our results show a tradeoff between speed and accuracy in the spatial memory task, with those individuals which were faster to move between cups in the test arena making more erroneous re-visits to cups that they had already checked for food. Furthermore, the accuracy of their carer predicted future survival, but not weight gain of the pups and the effect was contrary to expected, with pups that were cared for by less accurate individuals being more likely to survive to adulthood. Our research also provides evidence that while younger carers were less accurate during the test, the age of the carer did not have an impact on the chance of raising young that live to sexual maturity. Our findings suggest that banded mongoose carers' cognitive traits have fitness consequences for the young they care for, affecting the chance that these young live to maturity.

The social formation of fitness: lifetime consequences of prenatal nutrition and postnatal care in a wild mammal population.

Research in medicine and evolutionary biology suggests that the sequencing of parental investment has a crucial impact on offspring life history and health. Here, we take advantage of the synchronous birth system of wild banded mongooses to test experimentally the lifetime consequences to offspring of receiving extra investment prenatally versus postnatally. We provided extra food to half of the breeding females in each group during pregnancy, leaving the other half as matched controls. This manipulation resulted in two categories of experimental offspring in synchronously born litters: (i) 'prenatal boost' offspring whose mothers had been fed during pregnancy, and (ii) 'postnatal boost' offspring whose mothers were not fed during pregnancy but who received extra alloparental care in the postnatal period. Prenatal boost offspring lived substantially longer as adults, but postnatal boost offspring had higher lifetime reproductive success (LRS) and higher glucocorticoid levels across the lifespan. Both types of experimental offspring had higher LRS than offspring from unmanipulated litters. We found no difference between the two experimental categories of offspring in adult weight, age at first reproduction, oxidative stress or telomere lengths. These findings are rare experimental evidence that prenatal and postnatal investments have distinct effects in moulding individual life history and fitness in wild mammals. This article is part of the theme issue 'Evolutionary ecology of inequality'.

Characterization of genes with a putative key role in the parasitic lifestyle of the nematode Strongyloides ratti.

Parasitic nematodes are significant pathogens of humans and other animals. The molecular and genetic basis of animal parasitism is not yet fully understood. Strongyloides spp. are a genus of gastrointestinal nematodes of which species infect approximately 100­200 million people worldwide. S. ratti is a natural parasite of the rat, and a useful and amenable laboratory model. Previous EST and microarray analyses of the S. ratti life cycle have identified genes whose expression was specific, or biased, to the parasitic adult stage, suggesting that they may play a key role in parasitism in this species. Here we have further investigated the expression of these genes (by RT-PCR) throughout the S. ratti life-cycle. We produced recombinant proteins in vitro for a subset of these genes, which were used in Western blot analyses to investigate the distribution of the gene products among different stages of the S. ratti life cycle. We tested the efficacy of these recombinant proteins as anti-S. ratti vaccines. One of the proteins was detected in the excretory/secretory products of the parasitic stages.

Lung cancer incidence in Canadian petroleum workers.

OBJECTIVES: This study's purpose was to conduct a more in-depth analysis of the potential association between lung cancer, occupational exposures and smoking using data on cohort members from a Canadian petroleum company and refined statistical analyses. METHODS: Information on various exposures including asbestos and petroleum coke dust, as well as job type and operating segment were collected via manual and computerised company records. We performed life-table analyses, Poisson regression and restricted cubic splines to model exposure-response patterns while controlling for smoking status and age. Model diagnostics included the assessment of dispersion and offset parameters. RESULTS: These analyses show that lung cancer risk is strongly related to age and smoking, and to a lesser extent to province of last residence. When controlling for these covariates, there is suggestive evidence that maintenance work may also be related to lung cancer risk. Some analyses also indicate that asbestos exposure may be associated with lung cancer risk, although a clear exposure-response trend is not seen. Other exposures, including petroleum coke dust, were not strongly related to lung cancer risk, particularly when expressed as a continuous measure. CONCLUSIONS: These data suggest that maintenance work may be associated with lung cancer incidence, although exposures to the single agents studied did not emerge as strong predictors of lung cancer incidence. Maintenance work may be a surrogate for general exposures to several agents (eg, polycyclic aromatic hydrocarbons, metals, welding fumes, radiation, etc), although these results may be affected by residual confounding due to smoking or other socio-demographic factors.

Studies on the effect of temperature and pH on the inactivation of fish viral and bacterial pathogens.

Disposal of fish by-products in the European Community must comply with Regulation (EC) No 1069/2009 which categorizes animal by-products according to risk, and specifies methods of disposal of by-products according to that risk. There is provision under the regulation for composting or ensiling to be used for by-products from aquatic animals. Biosecurity considerations require knowledge of the parameters of time and temperature, or time and pH, required to inactivate any fish pathogens that may be present. To provide those data, we undertook laboratory studies on the inactivation of a number of fish pathogenic viruses and bacteria at 60 °C, pH 4.0 and pH 12.0 as a preliminary to conducting subsequent trials with the most resistant viruses and bacteria in fish tissues. The most resistant bacterium to 60 °C, pH 4.0 as well as pH 12.0 was Lactococcus garvieae. Its concentration was reduced to the level of sensitivity of the test after 24-48 h exposure to 60 °C, but it survived for at least 7 days at pH 4.0 and 14 days at pH 12.0. The most resistant virus to 60 °C was infectious pancreatic necrosis virus, and to pH 12.0 was infectious salmon anaemia virus. The majority of the viruses tested survived exposure to pH 4.0 for up to 28 days. The results suggest that the process of acid ensiling alone is not an effective method for the inactivation of many viral and bacterial pathogens, and fish by-products would need further treatment by a method approved under the regulation following ensiling, whereas alkaline or heat treatment are likely to provide an increased degree of biosecurity for on-farm processing of mortalities.

Leaders of war: modelling the evolution of conflict among heterogeneous groups.

War, in human and animal societies, can be extremely costly but can also offer significant benefits to the victorious group. We might expect groups to go into battle when the potential benefits of victory (V) outweigh the costs of escalated conflict (C); however, V and C are unlikely to be distributed evenly in heterogeneous groups. For example, some leaders who make the decision to go to war may monopolize the benefits at little cost to themselves ('exploitative' leaders). By contrast, other leaders may willingly pay increased costs, above and beyond their share of V ('heroic' leaders). We investigated conflict initiation and conflict participation in an ecological model where single-leader-multiple-follower groups came into conflict over natural resources. We found that small group size, low migration rate and frequent interaction between groups increased intergroup competition and the evolution of 'exploitative' leadership, while converse patterns favoured increased intragroup competition and the emergence of 'heroic' leaders. We also found evidence of an alternative leader/follower 'shared effort' outcome. Parameters that favoured high contributing 'heroic' leaders, and low contributing followers, facilitated transitions to more peaceful outcomes. We outline and discuss the key testable predictions of our model for empiricists studying intergroup conflict in humans and animals. This article is part of the theme issue 'Intergroup conflict across taxa'.