Enzymology under global change: organic nitrogen turnover in alpine and sub-Arctic soils

Understanding global change impacts on the globally important carbon storage in alpine, Arctic and sub-Arctic soils requires knowledge of the mechanisms underlying the balance between plant primary productivity and decomposition. Given that nitrogen availability limits both processes, understanding the response of the soil nitrogen cycle to shifts in temperature and other global change factors is crucial for predicting the fate of cold biome carbon stores. Measurements of soil enzyme activities at different positions of the nitrogen cycling network are an important tool for this purpose. We review a selection of studies that provide data on potential enzyme activities across natural, seasonal and experimental gradients in cold biomes. Responses of enzyme activities to increased nitrogen availability and temperature are diverse and seasonal dynamics are often larger than differences due to experimental treatments, suggesting that enzyme expression is regulated by a combination of interacting factors reflecting both nutrient supply and demand. The extrapolation from potential enzyme activities to prediction of elemental nitrogen fluxes under field conditions remains challenging. Progress in molecular '-omics' approaches may eventually facilitate deeper understanding of the links between soil microbial community structure and biogeochemical fluxes. In the meantime, accounting for effects of the soil spatial structure and in situ variations in pH and temperature, better mapping of the network of enzymatic processes and the identification of rate-limiting steps under different conditions should advance our ability to predict nitrogen fluxes.     

Variations in Amazon forest productivity correlated with foliar nutrients and modelled rates of photosynthetic carbon supply

The rate of above-ground woody biomass production, W(P), in some western Amazon forests exceeds those in the east by a factor of 2 or more. Underlying causes may include climate, soil nutrient limitations and species composition. In this modelling paper, we explore the implications of allowing key nutrients such as N and P to constrain the photosynthesis of Amazon forests, and also we examine the relationship between modelled rates of photosynthesis and the observed gradients in W(P). We use a model with current understanding of the underpinning biochemical processes as affected by nutrient availability to assess: (i) the degree to which observed spatial variations in foliar [N] and [P] across Amazonia affect stand-level photosynthesis; and (ii) how these variations in forest photosynthetic carbon acquisition relate to the observed geographical patterns of stem growth across the Amazon Basin. We find nutrient availability to exert a strong effect on photosynthetic carbon gain across the Basin and to be a likely important contributor to the observed gradient in W(P). Phosphorus emerges as more important than nitrogen in accounting for the observed variations in productivity. Implications of these findings are discussed in the context of future tropical forests under a changing climate.     

Biased estimates of clonal evolution and subclonal heterogeneity can arise from PCR duplicates in deep sequencing experiments

Accurate allele frequencies are important for measuring subclonal heterogeneity and clonal evolution. Deep-targeted sequencing data can contain PCR duplicates, inflating perceived read depth. Here we adapted the Illumina TruSeq Custom Amplicon kit to include single molecule tagging (SMT) and show that SMT-identified duplicates arise from PCR. We demonstrate that retention of PCR duplicate reads can imply clonal evolution when none exists, while their removal effectively controls the false positive rate. Additionally, PCR duplicates alter estimates of subclonal heterogeneity in tumor samples. Our method simplifies PCR duplicate identification and emphasizes their removal in studies of tumor heterogeneity and clonal evolution.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0420-4) contains supplementary material, which is available to authorized users.     

Sustained rheumatoid arthritis remission is uncommon in clinical practice

Introduction

Remission is an important goal of therapy in rheumatoid arthritis (RA), but data on duration of remission are lacking. Our objective was to describe the duration of remission in RA, assessed by different criteria.

Methods

We evaluated patients from the Brigham and Women''s Rheumatoid Arthritis Sequential Study (BRASS) not in remission at baseline with at least 2 years of follow-up. Remission was assessed according to the Disease Activity Score 28-C-reactive protein (DAS28-CRP4), Simplified Disease Activity Index (SDAI), and Clinical Disease Activity Index (CDAI) scores, and the recently proposed American College of Rheumatology (ACR)/European League against Rheumatism (EULAR) criteria for remission. Analyses were performed by using Kaplan-Meier survival curves.

Results

We identified 871 subjects with ≥2 years of follow-up. Of these subjects, 394 were in remission at one or more time-points and not in remission at baseline, according to at least one of the following criteria: DAS28-CRP < 2.6 (n = 309), DAS28-CRP < 2.3 (n = 275), SDAI (n = 168), CDAI (n = 170), and 2010 ACR/EULAR (n = 158). The median age for the 394 subjects at entrance to BRASS was 56 years; median disease duration was 8 years; 81% were female patients; and 72% were seropositive. Survival analysis performed separately for each remission criterion demonstrated that < 50% of subjects remained in remission 1 year later. Median remission survival time was 1 year. Kaplan-Meier curves of the various remission criteria did not significantly differ (P = 0.29 according to the log-rank test).

Conclusions

This study shows that in clinical practice, a minority of RA patients are in sustained remission.     

Identifying differentially methylated genes using mixed effect and generalized least square models

Background  

DNA methylation plays an important role in the process of tumorigenesis. Identifying differentially methylated genes or CpG islands (CGIs) associated with genes between two tumor subtypes is thus an important biological question. The methylation status of all CGIs in the whole genome can be assayed with differential methylation hybridization (DMH) microarrays. However, patient samples or cell lines are heterogeneous, so their methylation pattern may be very different. In addition, neighboring probes at each CGI are correlated. How these factors affect the analysis of DMH data is unknown.     

Genotypic comparison ofPantoea agglomeransplant and clinical strains

Background  

Pantoea agglomeransstrains are among the most promising biocontrol agents for a variety of bacterial and fungal plant diseases, particularly fire blight of apple and pear. However, commercial registration ofP. agglomeransbiocontrol products is hampered because this species is currently listed as a biosafety level 2 (BL2) organism due to clinical reports as an opportunistic human pathogen. This study compares plant-origin and clinical strains in a search for discriminating genotypic/phenotypic markers using multi-locus phylogenetic analysis and fluorescent amplified fragment length polymorphisms (fAFLP) fingerprinting.     

Historical biogeography and the evolution of the latitudinal gradient of species richness in the Papionini (Primata: Cercopithecidae)

We apply historical biogeography techniques to the macaques, baboons and their relatives (Primata: Papionini) and relate the inferred history of range shifts, and associated evolutionary events, to the latitudinal distribution of extant species, which is strongly tropical. The results of reversible parsimony, weighted ancestral area and dispersal-vicariance analyses all agree that Central Africa was part of the range of the ancestor of the tribe. Tropical regions with high current species richness (Central Africa, South-east Asia, Indonesia) have: (1) had a relatively long history of occupation, (2) experienced both a greater number and a greater average rate of speciation events and (3) given rise to more dispersal events to other regions. However, nested sister-taxon comparisons across the tribe show no overall association between differences in latitude and differences in rates of cladogenesis. Our historical reconstructions are largely consistent with previous hypotheses and fossil data, and suggest that both the passage of time since colonization and rates of cladogenesis have enhanced tropical species richness. Historical biogeography may thus considerably aid understanding of this and other spatial problems in macroecology.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 85 , 235–246.     

A histopathological and stereological study of liver damage in female rats caused by mercury vapor

We examined the possible effects of elemental mercury vapor on the liver of the female rats. We divided the animals into an untreated control group and an experimental group that was exposed to mercury vapor for 45 days. Liver samples were obtained for histological and stereological analysis. The total liver, parenchyma and sinusoid volumes were increased significantly in the mercury vapor treated group compared to controls. Also, the mean density, total number and mean nuclear diameter of hepatocytes, except for binucleated hepatocytes, was decreased in the experimental group compared to controls. Light and electron microscopy revealed alterations of liver structure of the experimental animals compared to controls.