The role of the local microbial ecosystem in respiratory health and disease

Respiratory tract infections are a major global health concern, accounting for high morbidity and mortality, especially in young children and elderly individuals. Traditionally, highly common bacterial respiratory tract infections, including otitis media and pneumonia, were thought to be caused by a limited number of pathogens including Streptococcus pneumoniae and Haemophilus influenzae. However, these pathogens are also frequently observed commensal residents of the upper respiratory tract (URT) and form—together with harmless commensal bacteria, viruses and fungi—intricate ecological networks, collectively known as the ‘microbiome’. Analogous to the gut microbiome, the respiratory microbiome at equilibrium is thought to be beneficial to the host by priming the immune system and providing colonization resistance, while an imbalanced ecosystem might predispose to bacterial overgrowth and development of respiratory infections. We postulate that specific ecological perturbations of the bacterial communities in the URT can occur in response to various lifestyle or environmental effectors, leading to diminished colonization resistance, loss of containment of newly acquired or resident pathogens, preluding bacterial overgrowth, ultimately resulting in local or systemic bacterial infections. Here, we review the current body of literature regarding niche-specific upper respiratory microbiota profiles within human hosts and the changes occurring within these profiles that are associated with respiratory infections.     

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.     

Lipotoxicity and steatohepatitis in an overfed mouse model for non-alcoholic fatty liver disease

The major risk factors for non-alcoholic fatty liver disease (NAFLD) are obesity, insulin resistance and dyslipidemia. The cause for progression from the steatosis stage to the inflammatory condition (non-alcoholic steatohepatitis (NASH)) remains elusive at present. Aim of this study was to test whether the different stages of NAFLD as well as the associated metabolic abnormalities can be recreated in time in an overfed mouse model and study the mechanisms underlying the transition from steatosis to NASH.Male C57Bl/6J mice were subjected to continuous intragastric overfeeding with a high-fat liquid diet (HFLD) for different time periods. Mice fed a solid high-fat diet (HFD) ad libitum served as controls. Liver histology and metabolic characteristics of liver, white adipose tisue (WAT) and plasma were studied.Both HFD-fed and HFLD-overfed mice initially developed liver steatosis, but only the latter progressed in time to NASH. NASH coincided with obesity, hyperinsulinemia, loss of liver glycogen and hepatic endoplasmatic reticulum stress. Peroxisome proliferator-activated receptor γ (Pparγ), fibroblast growth factor 21 (Fgf21), fatty acid binding protein (Fabp) and fatty acid translocase (CD36) were induced exclusively in the livers of the HFLD-overfed mice. Inflammation, reduced adiponectin expression and altered expression of genes that influence adipogenic capacity were only observed in WAT of HFLD-overfed mice.In conclusion: this dietary mouse model displays the different stages and the metabolic settings often found in human NAFLD. Lipotoxicity due to compromised adipose tissue function is likely associated with the progression to NASH, but whether this is cause or consequence remains to be established.     

The capsaicin receptor TRPV1 is a crucial mediator of the noxious effects of mustard oil

Mustard oil (MO) is a plant-derived irritant that has been extensively used in experimental models to induce pain and inflammation. The noxious effects of MO are currently ascribed to specific activation of the cation channel TRPA1 in nociceptive neurons. In contrast to this view, we show here that the capsaicin receptor TRPV1 has a surprisingly large contribution to aversive and pain responses and visceral irritation induced by MO. Furthermore, we found that this can be explained by previously unknown properties of this compound. First, MO has a bimodal effect on TRPA1, producing current inhibition at millimolar concentrations. Second, it directly and stably activates mouse and human recombinant TRPV1, as well as TRPV1 channels in mouse sensory neurons. Finally, physiological temperatures enhance MO-induced TRPV1 stimulation. Our results refute the dogma that TRPA1 is the sole nocisensor for MO and motivate a revision of the putative roles of these channels in models of MO-induced pain and inflammation. We propose that TRPV1 has a generalized role in the detection of irritant botanical defensive traits and in the coevolution of multiple mammalian and plant species.     

Factors influencing the seed source and sink functions of a floodplain nature reserve in the Netherlands

Question: How do species traits and abiotic factors influence the extent of hydrochorous dispersal into and out of a small floodplain area along a free‐flowing river in The Netherlands? Location: The Kappersbult nature reserve (53°07′28″N, 6°37′14″E), which is a floodplain along the Dutch River Drentsche Aa. Methods: Seeds transported by the river were collected in fine mesh nets for 24 consecutive hours once or twice a week for 1 year, upstream and downstream of the studied floodplain. Data on the captured seeds were related to species traits and abiotic factors and species composition in the floodplain. Results: The floodplain functioned both as a seed source and sink. High levels of river water seemed to promote seed transport to or from the floodplain. Seeds of riverbank species occurred significantly more often in the river water than expected. Net source species had significantly higher seed production, taller stature and higher seed buoyancy, but lower site elevation than net sink species. Seed weight was significantly higher for sink species than for other species. Conclusion: Our study found that inundation, and therefore more natural river water management, is a prerequisite for seed transport to and from a floodplain. The restoration of target floodplain vegetation may be successful for common species that produce many seeds and grow in proximity to the river. Consequently, it is expected that the probability of restoring vegetation types that occur further from the river, such as wet grasslands, by hydrochorous dispersal is low.     

Potential impacts of climate change on the environmental services of humid tropical alpine regions

Aim Humid tropical alpine environments are crucial ecosystems that sustain biodiversity, biological processes, carbon storage and surface water provision. They are identified as one of the terrestrial ecosystems most vulnerable to global environmental change. Despite their vulnerability, and the importance for regional biodiversity conservation and socio‐economic development, they are among the least studied and described ecosystems in the world. This paper reviews the state of knowledge about tropical alpine environments, and provides an integrated assessment of the potential threats of global climate change on the major ecosystem processes. Location Humid tropical alpine regions occur between the upper forest line and the perennial snow border in the upper regions of the Andes, the Afroalpine belt and Indonesia and Papua New Guinea. Results and main conclusions Climate change will displace ecosystem boundaries and strongly reduce the total area of tropical alpine regions. Displacement and increased isolation of the remaining patches will induce species extinction and biodiversity loss. Drier and warmer soil conditions will cause a faster organic carbon turnover, decreasing the below‐ground organic carbon storage. Since most of the organic carbon is currently stored in the soils, it is unlikely that an increase in above‐ground biomass will be able to offset soil carbon loss at an ecosystem level. Therefore a net release of carbon to the atmosphere is expected. Changes in precipitation patterns, increased evapotranspiration and alterations of the soil properties will have a major impact on water supply. Many regions are in danger of a significantly reduced or less reliable stream flow. The magnitude and even the trend of most of these effects depend strongly on local climatic, hydrological and ecological conditions. The extreme spatial gradients in these conditions put the sustainability of ecosystem management at risk.     

Allele-specific CAPS markers based on point mutations in resistance alleles at the pvr1 locus encoding eIF4E in Capsicum

Marker-assisted selection has been widely implemented in crop breeding and can be especially useful in cases where the traits of interest show recessive or polygenic inheritance and/or are difficult or impossible to select directly. Most indirect selection is based on DNA polymorphism linked to the target trait, resulting in error when the polymorphism recombines away from the mutation responsible for the trait and/or when the linkage between the mutation and the polymorphism is not conserved in all relevant genetic backgrounds. In this paper, we report the generation and use of molecular markers that define loci for selection using cleaved amplified polymorphic sequences (CAPS). These CAPS markers are based on nucleotide polymorphisms in the resistance gene that are perfectly correlated with disease resistance, the trait of interest. As a consequence, the possibility that the marker will not be linked to the trait in all backgrounds or that the marker will recombine away from the trait is eliminated. We have generated CAPS markers for three recessive viral resistance alleles used widely in pepper breeding, pvr1, pvr1 ¹, and pvr1 ². These markers are based on single nucleotide polymorphisms (SNPs) within the coding region of the pvr1 locus encoding an eIF4E homolog on chromosome 3. These three markers define a system of indirect selection for potyvirus resistance in Capsicum based on genomic sequence. We demonstrate the utility of this marker system using commercially significant germplasm representing two Capsicum species. Application of these markers to Capsicum improvement is discussed.