Gross Primary Productivity of a High Elevation Tropical Montane Cloud Forest

For decades, the productivity of tropical montane cloud forests (TMCF) has been assumed to be lower than in tropical lowland forests due to nutrient limitation, lower temperatures, and frequent cloud immersion, although actual estimates of gross primary productivity (GPP) are very scarce. Here, we present the results of a process-based modeling estimate of GPP, using a soil–plant–atmosphere model, of a high elevation Peruvian TMCF. The model was parameterized with field-measured physiological and structural vegetation variables, and driven with meteorological data from the site. Modeled transpiration corroborated well with measured sap flow, and simulated GPP added up to 16.2 ± SE 1.6 Mg C ha^?1 y^?1. Dry season GPP was significantly lower than wet season GPP, although this difference was 17% and not caused by drought stress. The strongest environmental controls on simulated GPP were variation of photosynthetic active radiation and air temperature (T _air). Their relative importance likely varies with elevation and the local prevalence of cloud cover. Photosynthetic parameters (V _cmax and J _max) and leaf area index were the most important non-environmental controls on GPP. We additionally compared the modeled results with a recent estimate of GPP of the same Peruvian TMCF derived by the summing of ecosystem respiration and net productivity terms, which added up to 26 Mg C ha^?1 y^?1. Despite the uncertainties in modeling GPP we conclude that at this altitude GPP is, conservatively estimated, 30–40% lower than in lowland rainforest and this difference is driven mostly by cooler temperatures than changes in other parameters.     

Consumers using the Internet for insomnia information: The who,what, and why

Information obtained from the Internet often influences the treatment choices of patients with insomnia. This study explored patterns of online information seeking and utilization among patients with insomnia. A total of 1013 participants took part in an online survey about sleep health information between July 2012 and March 2013. Participants also completed the Insomnia Severity Index and the Dysfunctional Beliefs and Attitudes about Sleep Scale. The results showed that those seeking insomnia-related information resources frequently searched online, and the information found appeared to influence important health behaviors such as treatment decisions, taking medication and whether to seek professional care. Information of interest revolved around insomnia treatment options and symptomology. While no predictors for Internet use were identified, the Internet does represent an important health-care portal for insomnia patients and warrants further investigation as targeted e-health interventions become more prominent in the routine management of insomnia.

     

Network medicine analysis of COPD multimorbidities

Background

Patients with chronic obstructive pulmonary disease (COPD) often suffer concomitant disorders that worsen significantly their health status and vital prognosis. The pathogenic mechanisms underlying COPD multimorbidities are not completely understood, thus the exploration of potential molecular and biological linkages between COPD and their associated diseases is of great interest.

Methods

We developed a novel, unbiased, integrative network medicine approach for the analysis of the diseasome, interactome, the biological pathways and tobacco smoke exposome, which has been applied to the study of 16 prevalent COPD multimorbidities identified by clinical experts.

Results

Our analyses indicate that all COPD multimorbidities studied here are related at the molecular and biological level, sharing genes, proteins and biological pathways. By inspecting the connections of COPD with their associated diseases in more detail, we identified known biological pathways involved in COPD, such as inflammation, endothelial dysfunction or apoptosis, serving as a proof of concept of the methodology. More interestingly, we found previously overlooked biological pathways that might contribute to explain COPD multimorbidities, such as hemostasis in COPD multimorbidities other than cardiovascular disorders, and cell cycle pathway in the association of COPD with depression. Moreover, we also observed similarities between COPD multimorbidities at the pathway level, suggesting common biological mechanisms for different COPD multimorbidities. Finally, chemicals contained in the tobacco smoke target an average of 69% of the identified proteins participating in COPD multimorbidities.

Conclusions

The network medicine approach presented here allowed the identification of plausible molecular links between COPD and comorbid diseases, and showed that many of them are targets of the tobacco exposome, proposing new areas of research for understanding the molecular underpinning of COPD multimorbidities.

Electronic supplementary material

The online version of this article (doi:10.1186/s12931-014-0111-4) contains supplementary material, which is available to authorized users.     

An Immunochip-based interrogation of scleroderma susceptibility variants identifies a novel association at DNASE1L3

Introduction

The aim of the study was to interrogate the genetic architecture and autoimmune pleiotropy of scleroderma susceptibility in the Australian population.

Methods

We genotyped individuals from a well-characterized cohort of Australian scleroderma patients with the Immunochip, a custom array enriched for single nucleotide polymorphisms (SNPs) at immune loci. Controls were taken from the 1958 British Birth Cohort. After data cleaning and adjusting for population stratification the final dataset consisted of 486 cases, 4,458 controls and 146,525 SNPs. Association analyses were conducted using logistic regression in PLINK. A replication study was performed using 833 cases and 1,938 controls.

Results

A total of eight loci with suggestive association (P <10^-4.5) were identified, of which five showed significant association in the replication cohort (HLA-DRB1, DNASE1L3, STAT4, TNP03-IRF5 and VCAM1). The most notable findings were at the DNASE1L3 locus, previously associated with systemic lupus erythematosus, and VCAM1, a locus not previously associated with human disease. This study identified a likely functional variant influencing scleroderma susceptibility at the DNASE1L3 locus; a missense polymorphism rs35677470 in DNASE1L3, with an odds ratio of 2.35 (P = 2.3 × 10⁻¹⁰) in anti-centromere antibody (ACA) positive cases.

Conclusions

This pilot study has confirmed previously reported scleroderma associations, revealed further genetic overlap between scleroderma and systemic lupus erythematosus, and identified a putative novel scleroderma susceptibility locus.

Electronic supplementary material

The online version of this article (doi:10.1186/s13075-014-0438-8) contains supplementary material, which is available to authorized users.     

A meta-analysis of the risk of venous thromboembolism in inflammatory rheumatic diseases

Introduction

We performed a meta-analysis to investigate the risk of deep vein thrombosis (DVT) and/or pulmonary embolisms (PEs) in patients with inflammatory arthritis, vasculitis and connective tissue diseases (CTDs) (systemic lupus erythematosus (SLE), Sjögren’s syndrome, inflammatory myositis and systemic sclerosis (SSc)).

Methods

PubMed, Embase, the Cochrane databases and MEDLINE were searched to identify full-text English-language publications about adult patients with rheumatologic inflammatory diseases and venous thromboembolisms (VTEs). Data regarding rates of DVTs and PEs were extracted. Using random-effects models, pooled estimates for VTEs in individual and pooled diseases were compared with matched populations where possible. Studies were excluded if VTEs were described in the setting of pregnancy, postoperative outcomes or solely antiphospholipid antibody syndrome.

Results

Most of the 5,206 studies were excluded because they did not state the rate or incidence of VTEs. In total, 25 studies remained for analysis. Ten studies that included rheumatoid arthritis comprised an aggregate of 5,273,942 patients and 891,530,181 controls with a cumulative VTE incidence of 2.18% (95% confidence interval (CI): 1.82% to 2.54%) and an odds ratio of 2.23 (95% CI: 2.02 to 2.47) compared to age- and sex-matched populations. Ten studies comprised an aggregate of 54,697 SLE patients with a cumulative VTE incidence of 7.29% (95% CI: 5.82% to 8.75%). Four Sjögren’s syndrome studies comprising an aggregate of 25,100 patients demonstrated a cumulative VTE incidence of 2.18% (95% CI: 0.79% to 3.57%). Four studies of inflammatory myositis comprising an aggregate of 8,245 patients yielded a cumulative VTE incidence of 4.03% (95% CI: 2.38% to 5.67%). The SSc- and antineutrophil cytoplasmic antibody vasculitis–related cumulative VTE rates (four studies each) were 3.13% and 7.97%, respectively.

Conclusions

The inflammatory rheumatologic diseases studied were all associated with high rates of VTEs—more than three times higher than in the general population.

Electronic supplementary material

The online version of this article (doi:10.1186/s13075-014-0435-y) contains supplementary material, which is available to authorized users.     

Evidence of population bottleneck in Astragalus michauxii (Fabaceae), a narrow endemic of the southeastern United States

Genetic factors such as decreased genetic diversity and increased homozygosity can have detrimental effects on rare species, and may ultimately limit potential adaptation and exacerbate population declines. The Gulf and Atlantic Coastal Plain physiographic region has the second highest level of endemism in the continental USA, but habitat fragmentation and land use changes have resulted in catastrophic population declines for many species. Astragalus michauxii (Fabaceae) is an herbaceous plant endemic to the region that is considered vulnerable to extinction, with populations generally consisting of fewer than 20 individuals. We developed eight polymorphic microsatellites and genotyped 355 individuals from 24 populations. We characterized the population genetic diversity and structure, tested for evidence of past bottlenecks, and identified evidence of contemporary gene flow between populations. The mean ratios of the number of alleles to the allelic range (M ratio) across loci for A. michauxii populations were well below the threshold of 0.68 identified as indicative of a past genetic bottleneck. Genetic diversity estimates were similar across regions and populations, and comparable to other long-lived perennial species. Within-population genetic variation accounted for 92 % of the total genetic variation found in the species. Finally, there is evidence for contemporary gene flow among the populations in North Carolina. Although genetic factors can threaten rare species, maintaining habitats through prescribed burning, in concert with other interventions such as population augmentation or (re)introduction, are likely most critical to the long term survival of A. michauxii.     

Development and testing of a genetic marker‐based pedigree reconstruction system ‘PR‐genie’ incorporating size‐class data

For wildlife populations, it is often difficult to determine biological parameters that indicate breeding patterns and population mixing, but knowledge of these parameters is essential for effective management. A pedigree encodes the relationship between individuals and can provide insight into the dynamics of a population over its recent history. Here, we present a method for the reconstruction of pedigrees for wild populations of animals that live long enough to breed multiple times over their lifetime and that have complex or unknown generational structures. Reconstruction was based on microsatellite genotype data along with ancillary biological information: sex and observed body size class as an indicator of relative age of individuals within the population. Using body size‐class data to infer relative age has not been considered previously in wildlife genealogy and provides a marked improvement in accuracy of pedigree reconstruction. Body size‐class data are particularly useful for wild populations because it is much easier to collect noninvasively than absolute age data. This new pedigree reconstruction system, PR‐genie, performs reconstruction using maximum likelihood with optimization driven by the cross‐entropy method. We demonstrated pedigree reconstruction performance on simulated populations (comparing reconstructed pedigrees to known true pedigrees) over a wide range of population parameters and under assortative and intergenerational mating schema. Reconstruction accuracy increased with the presence of size‐class data and as the amount and quality of genetic data increased. We provide recommendations as to the amount and quality of data necessary to provide insight into detailed familial relationships in a wildlife population using this pedigree reconstruction technique.