Multi‐scale habitat modification by coexisting ecosystem engineers drives spatial separation of macrobenthic functional groups

By changing habitat conditions, ecosystem engineers increase niche diversity and have profound effects on the distribution and abundances of other organisms. Although many ecosystems contain several engineering species, it is still unclear how the coexistence of multiple engineers affects the physical habitat and the structure of the community on a landscape scale. Here, we investigated through a large‐scale field manipulation how three coexisting engineers on intertidal flats (cockles Cerastoderma edule; lugworms Arenicola marina; blue mussels Mytilus edulis) influence the functional composition of the local macrobenthic community and what the consequences are at the landscape level. By using biological trait analysis (BTA), we show that on the local scale biogenic changes in sediment accumulation and organic matter content translated into specific shifts in the distribution of functional traits within the community. At a landscape scale, the co‐occurrence of multiple ecosystem engineers resulted in the spatial separation of different functional groups, i.e. different functional groups dominated unique complementary habitats. Our results emphasize the role of co‐occurring multiple engineers in shaping natural communities, thus contributing to a better knowledge of community assembly rules. This understanding can profitably be used to improve ecosystem‐based management and conservation actions.     

Optimisation of a quantitative polymerase chain reaction-based strategy for the detection and quantification of human herpesvirus 6 DNA in patients undergoing allogeneic haematopoietic stem cell transplantation

Human herpesvirus 6 (HHV-6) may cause severe complications after haematopoietic stem cell transplantation (HSCT). Monitoring this virus and providing precise, rapid and early diagnosis of related clinical diseases, constitute essential measures to improve outcomes. A prospective survey on the incidence and clinical features of HHV-6 infections after HSCT has not yet been conducted in Brazilian patients and the impact of this infection on HSCT outcome remains unclear. A rapid test based on real-time quantitative polymerase chain reaction (qPCR) has been optimised to screen and quantify clinical samples for HHV-6. The detection step was based on reaction with TaqMan^® hydrolysis probes. A set of previously described primers and probes have been tested to evaluate efficiency, sensitivity and reproducibility. The target efficiency range was 91.4% with linearity ranging from 10-10⁶ copies/reaction and a limit of detection of five copies/reaction or 250 copies/mL of plasma. The qPCR assay developed in the present study was simple, rapid and sensitive, allowing the detection of a wide range of HHV-6 loads. In conclusion, this test may be useful as a practical tool to help elucidate the clinical relevance of HHV-6 infection and reactivation in different scenarios and to determine the need for surveillance.     

Apparent annual survival of staging ruffs during a period of population decline: insights from sex and site-use related differences

The ruff Philomachus pugnax, a lekking shorebird wintering in Africa and breeding across northern Eurasia, declined severely in its western range. Based on a capture-mark-resighting programme (2004–2011) in the westernmost staging area in Friesland (the Netherlands), we investigated changes in apparent annual survival in relation to age and sex to explore potential causes of decline. We also related temporal variation in apparent survival to environmental factors. We used the Capture-Mark-Recapture multievent statistical framework to overcome biases in survival estimates after testing for hidden heterogeneity of detection. This enabled the estimation of the probability to belong to high or low detectability classes. Apparent survival varied between years but was not related to weather patterns along the flyway, or to flood levels in the Sahel. Over time, a decline in apparent survival is suggested. Due to a short data series and flag loss in the last period this cannot be verified. Nevertheless, the patterns in sex-specific detectability and survival lead to new biological insights. Among highly detectable birds, supposedly most reliant on Friesland, males survived better than females ( = 0.74, range 0.51–0.93; = 0.51, range 0.24–0.81). Among low detectable birds, the pattern is reversed ( = 0.64, range 0.37–0.89; = 0.73, range 0.48–0.93). Probably the staging population contains a mixture of sex-specific migration strategies. A loss of staging females could greatly affect the dynamics of the western ruff population. Further unravelling of these population processes requires geographically extended demographic monitoring and the use of tracking devices.     

Association of 25-Hydroxyvitamin D status and genetic variation in the vitamin D metabolic pathway with FEV1 in the Framingham Heart Study

Background

Vitamin D is associated with lung function in cross-sectional studies, and vitamin D inadequacy is hypothesized to play a role in the pathogenesis of chronic obstructive pulmonary disease. Further data are needed to clarify the relation between vitamin D status, genetic variation in vitamin D metabolic genes, and cross-sectional and longitudinal changes in lung function in healthy adults.

Methods

We estimated the association between serum 25-hydroxyvitamin D [25(OH)D] and cross-sectional forced expiratory volume in the first second (FEV₁) in Framingham Heart Study (FHS) Offspring and Third Generation participants and the association between serum 25(OH)D and longitudinal change in FEV₁ in Third Generation participants using linear mixed-effects models. Using a gene-based approach, we investigated the association between 241 SNPs in 6 select vitamin D metabolic genes in relation to longitudinal change in FEV₁ in Offspring participants and pursued replication of these findings in a meta-analyzed set of 4 independent cohorts.

Results

We found a positive cross-sectional association between 25(OH)D and FEV₁ in FHS Offspring and Third Generation participants (P = 0.004). There was little or no association between 25(OH)D and longitudinal change in FEV₁ in Third Generation participants (P = 0.97). In Offspring participants, the CYP2R1 gene, hypothesized to influence usual serum 25(OH)D status, was associated with longitudinal change in FEV₁ (gene-based P < 0.05). The most significantly associated SNP from CYP2R1 had a consistent direction of association with FEV₁ in the meta-analyzed set of replication cohorts, but the association did not reach statistical significance thresholds (P = 0.09).

Conclusions

Serum 25(OH)D status was associated with cross-sectional FEV₁, but not longitudinal change in FEV₁. The inconsistent associations may be driven by differences in the groups studied. CYP2R1 demonstrated a gene-based association with longitudinal change in FEV₁ and is a promising candidate gene for further studies.

Electronic supplementary material

The online version of this article (doi:10.1186/s12931-015-0238-y) contains supplementary material, which is available to authorized users.     

Comparative proteomics of colon cancer stem cells and differentiated tumor cells identifies BIRC6 as a potential therapeutic target

Patients with liver metastases from colon carcinoma show highly variable responses to chemotherapy and tumor recurrence is frequently observed. Therapy-resistant cancer stem cells have been implicated in drug resistance and tumor recurrence. However, the factors determining therapy resistance and tumor recurrence are poorly understood. The aim of this study was to gain insight into these mechanisms by comparing the proteomes of patient-derived cancer stem cell cultures and their differentiated isogenic offspring. We established colonosphere cultures derived from resection specimens of liver metastases in patients with colon cancer. These colonospheres, enriched for colon cancer stem cells, were used to establish isogenic cultures of stably differentiated nontumorigenic progeny. Proteomics based on one-dimensional gel electrophoresis coupled to nano liquid chromatography tandem MS was used to identify proteome differences between three of these paired cultures. The resulting data were analyzed using Ingenuity Pathway Software. Out of a total data set of 3048 identified proteins, 32 proteins were at least twofold up-regulated in the colon cancer stem cells when compared with the differentiated cells. Pathway analysis showed that "cell death " regulation is strikingly different between the two cell types. Interestingly, one of the top-up-regulated proteins was BIRC6, which belongs to the class of Inhibitor of Apoptosis Proteins. Knockdown of BIRC6 sensitized colon cancer stem cells against the chemotherapeutic drugs oxaliplatin and cisplatin. This study reveals that differentiation of colon cancer stem cells is accompanied by altered regulation of cell death pathways. We identified BIRC6 as an important mediator of cancer stem cell resistance against cisplatin and oxaliplatin. Targeting BIRC6, or other Inhibitors of Apoptosis Proteins, may help eradicating colon cancer stem cells.     

A global population redistribution in a migrant shorebird detected with continent‐wide qualitative breeding survey data

Aim Over the last two decades, thousands of northward migrating ruffs (Philomachus pugnax) have disappeared from western European staging sites. These migratory ruffs were partly temperate breeding birds, but most individuals head towards the Eurasian Arctic tundras where 95% of the global population breeds. This regional decline may represent either: (1) local loss of breeding birds in western Europe, (2) a global decline, (3) shift(s) in distribution or (4) a combination of these. Location Northern Eurasia. Methods To put the declines in western Europe in context, we analysed Arctic monitoring data from the last two decades ( Soloviev & Tomkovich, 2009 ) to detect changes in regional breeding densities across northern Eurasia. We used a novel approach applying generalized additive modelling (GAM) and generalized estimations equations (GEE). Results We show that the global breeding population of ruffs has made a significant eastwards shift into the Asian part of the breeding range. In the European Arctic, ruffs decreased during the last 18 years. At the same time, in western Siberia, ruffs increased. In eastern Siberia, no significant population changes could be detected. These changes corroborate the finding that during northward migration, growing numbers of ruffs avoided staging areas in the Netherlands and Sweden and started migrating along a more easterly route leading into western Siberia. Main conclusions We detected an unprecedented large‐scale population redistribution of ruffs and suggest that this is a response to loss of habitat quality at the traditional staging site in the Netherlands.     

Do Uniparental Sanderlings Calidris alba Increase Egg Heat Input to Compensate for Low Nest Attentiveness?

Birds breeding in cold environments regularly have to interrupt incubation to forage, causing a trade-off between two mutually exclusive behaviours. Earlier studies showed that uniparental Arctic sandpipers overall spend less time incubating their eggs than biparental species, but interspecific differences in size and ecology were potential confounding factors. This study reports on a within-species comparison of breeding schedules and metal egg temperatures in uni- and biparental sanderlings (Calidris alba) in Northeast Greenland in relation to ambient temperature. We recorded incubation schedules with nest temperature loggers in 34 sanderling clutches (13 uniparentals, 21 biparentals). The temperature of a metal egg placed within the clutch of 17 incubating birds (6 uniparentals, 9 biparentals) was measured as an indicator of the heat put into eggs. Recess frequency, recess duration and total recess time were higher in uniparentals than in biparentals and positively correlated with ambient temperatures in uniparentals only. Uniparental sanderlings maintained significantly higher metal egg temperatures during incubation than biparentals (1.4°C difference on average). Our results suggest that uniparental sanderlings compensate for the lower nest attendance, which may prolong the duration of the incubation period and negatively affect the condition of the hatchlings, by maintaining a higher heat flux into the eggs.     

Rtt107/Esc4 binds silent chromatin and DNA repair proteins using different BRCT motifs

Background  

By screening a plasmid library for proteins that could cause silencing when targeted to the HMR locus in Saccharomyces cerevisiae, we previously reported the identification of Rtt107/Esc4 based on its ability to establish silent chromatin. In this study we aimed to determine the mechanism of Rtt107/Esc4 targeted silencing and also learn more about its biological functions.     

Plasma metabolites reflect seasonally changing metabolic processes in a long-distance migrant shorebird (Calidris canutus)

Migrant birds have tightly scheduled annual cycles consisting of several distinct life cycle (sub-)stages such as reproduction, migration, moult and overwintering, each of which have specific metabolic requirements (e.g., fattening during migration, protein build-up during moult). This study examines changes in fat and protein metabolism during the annual cycle of body mass and moult over 1.5 years in a captive flock of an arctic-breeding shorebird, the red knot Calidris canutus islandica. 2-5 h after food withdrawal, plasma uric acid levels were still decreasing and beta-hydroxy-butyrate levels were low, indicating prolonged catabolism of dietary protein, probably linked with a conversion into lipids. Such a late-resorptive state is achieved much earlier in passerines, but only after several days in penguins and, thus, seems to depend on meal size or mass-specific metabolic rate. Substages of body mass gain and high body mass were characterized by increased plasma triglyceride levels reflecting increased turnover of lipids, and low levels of the ketone body beta-hydroxy- butyrate, indicating that the bird is not short of glucose. The high uric acid levels during these substages indicated an increased breakdown of nutritional protein. During moult, plasma triglyceride levels were low, suggesting that lipids were less available than at other times of the year. It is concluded that plasma metabolite levels indicate the metabolic processes related to migratory fuelling and moult and the influence of exogeneous factors.