Factors determining plant species richness in Alaskan arctic tundra

Abstract. We studied the relationship between plant N:P ratio, soil characteristics and species richness in wet sedge and tussock tundra in northern Alaska at seven sites. We also collected data on soil characteristics, above‐ground biomass, species richness and composition. The N:P ratio of the vegetation did not show any relationship with species richness. The N:P ratio of the soil was related with species richness for both vegetation types. Species richness in the tussock tundra was most strongly correlated with soil calcium content and soil pH, with a strong correlation between these two factors. N:P ratio of the soil was also correlated with soil pH. Other factors correlated with species richness were soil moisture and Sphagnum cover. Organic matter content was the factor most strongly correlated with species richness in the wet sedge vegetation. N:P ratio of the soil was strongly correlated with organic matter content. We conclude that N:P ratio in the vegetation is not an important factor determining species richness in arctic tundra and that species richness in arctic tundra is mainly determined by pH and flooding. In tussock tundra the pH, declining with soil age, in combination with Sphagnum growth strongly decreases species richness, while in wet sedge communities flooding over long periods of time creates less favourable conditions for species richness.     

The second and third optic ganglia of the worker bee

Summary The gross morphology and the fine-structural characteristics of neurones of the second and third optic ganglia of the honeybee Apis mellifera were investigated light microscopically on the basis of Golgi (selective silver)- and reduced silver preparations.The second optic ganglion, the medulla, is ovoid in shape and has a slightly convex distal surface and a slightly concave proximal surface. The medullar outer levels are characteristically composed of neuronal arrangements showing strict precision of their geometrical spacing proximally as far as a pronounced layer of tangential fibre elements comprising the serpentine layer of the medulla. At the inner medullary levels retinotopic channels are again multiplied, and the arrangement of axons and dendrites contribute to a complex lattice.The third optic ganglion, the lobula, is interposed between the medulla and the protocerebrum. It is the site of termination of the third-order neurones. The lobula in hymenopterans appears, in contrast to dipterans, odonates and lepidopterans, as a single neuropilic mass.A short review of the electrophysiological data concerning these two ganglia has been tentatively correlated with some of the anatomical data.     

Estimates of missing heritability for complex traits in Brown Swiss cattle

Background

Genomic selection estimates genetic merit based on dense SNP (single nucleotide polymorphism) genotypes and phenotypes. This requires that SNPs explain a large fraction of the genetic variance. The objectives of this work were: (1) to estimate the fraction of genetic variance explained by dense genome-wide markers using 54 K SNP chip genotyping, and (2) to evaluate the effect of alternative marker-based relationship matrices and corrections for the base population on the fraction of the genetic variance explained by markers.

Methods

Two alternative marker-based relationship matrices were estimated using 35 706 SNPs on 1086 dairy bulls. Both pedigree- and marker-based relationship matrices were fitted simultaneously or separately in an animal model to estimate the fraction of variance not explained by the markers, i.e. the fraction explained by the pedigree. The phenotypes considered in the analysis were the deregressed estimated breeding values (dEBV) for milk, fat and protein yield and for somatic cell score (SCS).

Results

When dEBV were not sufficiently accurate (50 or 70%), the estimated fraction of the genetic variance explained by the markers was around 65% for yield traits and 45% for SCS. Scaling marker genotypes with locus-specific frequencies of heterozygotes slightly increased the variance explained by markers, compared with scaling with the average frequency of heterozygotes across loci. The estimated fraction of the genetic variance explained by the markers using separately both relationships matrices followed the same trends but the results were underestimated. With less accurate dEBV estimates, the fraction of the genetic variance explained by markers was underestimated, which is probably an artifact due to the dEBV being estimated by a pedigree-based animal model.

Conclusions

When using only highly accurate dEBV, the proportion of the genetic variance explained by the Illumina 54 K SNP chip was approximately 80% for Brown Swiss cattle. These results depend on the SNP chip used and the family structure of the population, i.e. more dense SNPs and closer family relationships are expected to result in a higher fraction of the variance explained by the SNPs.     

Two-phase resolution of polyploidy in the Arabidopsis metabolic network gives rise to relative and absolute dosage constraints

The abundance of detected ancient polyploids in extant genomes raises questions regarding evolution after whole-genome duplication (WGD). For instance, what rules govern the preservation or loss of the duplicated genes created by WGD? We explore this question by contrasting two possible preservation forces: selection on relative and absolute gene dosages. Constraints on the relative dosages of central network genes represent an important force for maintaining duplicates (the dosage balance hypothesis). However, preservation may also result from selection on the absolute abundance of certain gene products. The metabolic network of the model plant Arabidopsis thaliana is a powerful system for comparing these hypotheses. We analyzed the surviving WGD-produced duplicate genes in this network, finding evidence that the surviving duplicates from the most recent WGD (WGD-α) are clustered in the network, as predicted by the dosage balance hypothesis. A flux balance analysis suggests an association between the survival of duplicates from a more ancient WGD (WGD-β) and reactions with high metabolic flux. We argue for an interplay of relative and absolute dosage constraints, such that the relative constraints imposed by the recent WGD are still being resolved by evolution, while they have been essentially fully resolved for the ancient event.     

Higher Chlamydia trachomatis Prevalence in Ethnic Minorities Does Not Always Reflect Higher Sexual Risk Behaviour

Background

In affluent countries, the prevalence of Chlamydia trachomatis (CT) is often higher in certain ethnic minorities than in the majority population. In the Netherlands, we examined why CT prevalence is higher in Surinamese/Antilleans, the largest minority in the country.

Methods

Heterosexuals were recruited for a cross-sectional survey from May through August 2010 at the sexually transmitted infections (STI) clinic in Amsterdam. Participants completed a questionnaire and were tested for STI. A causal directed acyclic graph was assumed to investigate whether the association between ethnicity and CT could be explained by differences in sexual risk behaviour and socio-economic status.

Results

Subjects included 1044 with Dutch background and 335 with Surinamese/Antillean background. Median age for the combined population was 25 (IQR 22-30) years, and 55.4% was female. Sexual risk behaviour did not differ significantly between the two groups. CT was diagnosed in 17.9% of Surinamese/Antilleans and in 11.4% of Dutch. Surinamese/Antilleans were significantly more likely to have CT (OR 1.70; 95% CI 1.21-2.38). The association between ethnicity and CT remained statistically significant after adjusting for sexual risk behaviour, age, sex, and ethnic mixing (aOR 1.48; 95% CI 1.00-2.18), but not after adjusting for education and neighbourhood, markers of socio-economic status (aOR 1.08; 95% CI 0.71-1.64).

Conclusion

The difference in CT prevalence between the minority and majority groups was not explained by differences in sexual risk behaviour. The higher CT prevalence found among Surinamese/Antilleans appeared to reflect their lower educational level and neighbourhood, two markers of lower socio-economic status. We hypothesise that the effect results from lower health-seeking behaviour.     

The value of glucocorticoid co-therapy in different rheumatic diseases - positive and adverse effects

Glucocorticoids play a pivotal role in the management of many inflammatory rheumatic diseases. The therapeutic effects range from pain relief in arthritides, to disease-modifying effects in early rheumatoid arthritis, and to strong immunosuppressive actions in vasculitides and systemic lupus erythematosus. There are multiple indications that adverse effects are more frequent with the longer use of glucocorticoids and use of higher dosages, but high-quality data on the occurrence of adverse effects are scarce especially for dosages above 10 mg prednisone daily. The underlying rheumatic disease, disease activity, risk factors and individual responsiveness of the patient should guide treatment decisions. Monitoring for adverse effects should also be tailored to the patient. Continuously balancing the benefits and risks of glucocorticoid therapy is recommended. There is an ongoing quest for new drugs with glucocorticoid actions without the potential to cause harmful effects, such as selective glucocorticoid receptor agonists, but the application of a new compound in clinical practice will probably not occur within the next few years. In the meantime, basic research on glucocorticoid effects and detailed reports on therapeutic efficacy and occurrence of adverse effects will be valuable in weighing benefits and risks in clinical practice.     

Design and baseline characteristics of the ParkFit study,a randomized controlled trial evaluating the effectiveness of a multifaceted behavioral program to increase physical activity in Parkinson patients

Background  

Many patients with Parkinson's disease (PD) lead a sedentary lifestyle. Promotion of physical activities may beneficially affect the clinical presentation of PD, and perhaps even modify the course of PD. However, because of physical and cognitive impairments, patients with PD require specific support to increase their level of physical activity.     

The relation between insulin resistance and hemostasis: pleiotropic genes and common environment.

Risk factors for coronary heart disease (CHD), including prethrombotic changes in hemostasis, cluster with the insulin resistance (IR) syndrome. The aim of the present study was to investigate to what extent the relation between IR and hemostatic risk factors is due to shared genes or environmental factors. Multivariate genetic analysis was performed using a total of 314 (107 monozygotic and 207 dizygotic) twin pairs on IR assessed by HOMA, fibrinogen, plasminogen activator inhibitor (PAI-1), tissue plasminogen activator (tPA), factor VIII (FVIII), von Willebrand factor (vWF) and factor XIII B-subunit. The relationship between IR and the 6 hemostatic factors could best be explained by an independent pathway model consisting of 2 common genetic factors, one of which influenced IR and all hemostatic factors, and 3 common environmental factors, each representing the shared variance between IR and different aspects of the hemostatic system. Genetic correlations between IR and hemostatic proteins were larger than their environmental counterparts. Since IR and prethrombotic changes are features of both diabetes and CHD, the finding of one set of pleiotropic genes warrants the identification of these common pathways which may provide new avenues for treatment and prevention of both diabetes and CHD.     

The Prognostic Value of Microsatellite Instability,KRAS, BRAF and PIK3CA Mutations in Stage II Colon Cancer Patients

In the era of personalized cancer medicine, identifying mutations within patient tumors plays an important role in defining high-risk stage II colon cancer patients. The prognostic role of BRAF V600E mutation, microsatellite instability (MSI) status, KRAS mutation and PIK3CA mutation in stage II colon cancer patients is not settled. We retrospectively analyzed 186 patients with stage II colon cancer who underwent an oncological resection but were not treated with adjuvant chemotherapy. KRAS mutations, PIK3CA mutation, V600E BRAF mutation and MSI status were determined. Survival analyses were performed. Mutations were found in the patients with each mutation in the following percentages: 23% (MSI), 35% (KRAS), 19% (BRAF) and 11% (PIK3CA). A trend toward worse overall survival (OS) was seen in patients with an MSI (5-year OS 74% versus 82%, adjusted hazard ratio [HR] 1.8, 95% confidence interval [CI] 0.6–4.9) and a KRAS-mutated tumor (5-year OS 77% versus 82%, adjusted HR 1.7, 95% CI 0.8–3.5). MSI and BRAF-mutated tumors tended to correlate with poorer disease-free survival (DFS) (5-year DFS 60% versus 78%, adjusted HR 1.6, 95% CI 0.5–2.1 and 5-year DFS 57% versus 77%, adjusted HR 1.1, 95% CI 0.4–2.6 respectively). In stage II colon cancer patients not treated with adjuvant chemotherapy, BRAF mutation and MSI status both tended to have a negative prognostic effect on disease-free survival. KRAS and MSI status also tended to be correlated with worse overall survival.