Effects of wood ash and nitrogen fertilization on fine root biomass and soil and foliage nutrients in a Norway spruce stand in Finland

We determined the effects of wood ash fertilization, given together with nitrogen (WAN), and nitrogen given together with P, B and Cu (SSF), on soil and foliage nutrients and fine root biomass in a 45-year-old Norway spruce stand in southern Finland. Fine roots were sampled 9 years, and the soil 10 years after ash (3 t/ha) and nitrogen (150 kg/ha) application. Fine root biomass tended to be lower, the necromass higher, and the fine root distribution relatively deeper on the WAN than on the control and SSF plots. The response of fine root biomass to WAN was probably related to changes in soil acidity. pH, base saturation, total and extractable concentrations of Ca, K, Mg and P, and total B, Cd, Mn, Ni and Zn concentrations in the organic layer were significantly higher on the WAN plots than on the SSF and the control plots with no ash and nutrient addition. On the WAN plots, the pH was 1.2 pH-units higher, the exchangeable Ca concentrations fourfold and those of Mg over twofold compared to the control plots. WAN increased the concentrations of K but decreased those of Mn and Ni in the needles compared to the control and SSF treatment. Even though ash and nitrogen fertilisation tended to decrease the fine root biomass, this decrease was not likely to affect tree growth during a 10-year period.     

Local IL-13 gene transfer prior to immune-complex arthritis inhibits chondrocyte death and matrix-metalloproteinase-mediated cartilage matrix degradation despite enhanced joint inflammation

During immune-complex-mediated arthritis (ICA), severe cartilage destruction is mediated by Fcγ receptors (FcγRs) (mainly FcγRI), cytokines (e.g. IL-1), and enzymes (matrix metalloproteinases (MMPs)). IL-13, a T helper 2 (Th2) cytokine abundantly found in synovial fluid of patients with rheumatoid arthritis, has been shown to reduce joint inflammation and bone destruction during experimental arthritis. However, the effect on severe cartilage destruction has not been studied in detail. We have now investigated the role of IL-13 in chondrocyte death and MMP-mediated cartilage damage during ICA. IL-13 was locally overexpressed in knee joints after injection of an adenovirus encoding IL-13 (AxCAhIL-13), 1 day before the onset of arthritis; injection of AxCANI (an empty adenoviral construct) was used as a control. IL-13 significantly increased the amount of inflammatory cells in the synovial lining and the joint cavity, by 30% to 60% at day 3 after the onset of ICA. Despite the enhanced inflammatory response, chondrocyte death was diminished by two-thirds at days 3 and 7. The mRNA level of FcγRI, a receptor shown to be crucial in the induction of chondrocyte death, was significantly down-regulated in synovium. Furthermore, MMP-mediated cartilage damage, measured as neoepitope (VDIPEN) expression using immunolocalization, was halved. In contrast, mRNA levels of MMP-3, -9, -12, and -13 were significantly higher and IL-1 protein, which induces production of latent MMPs, was increased fivefold by IL-13. This study demonstrates that IL-13 overexpression during ICA diminished both chondrocyte death and MMP-mediated VDIPEN expression, even though joint inflammation was enhanced.     

Stress indications in copper- and nickel-exposed Scots pine seedlings

Scots pine nursery seedlings were planted in pots, five seedlings per treatment, and placed in an experimental field at the University of Oulu in northern Finland at the beginning of June 1997. Copper and nickel sulphates were mixed with forest mineral soil before seedling planting. The metal levels ranged from 0 to 25 mg Ni kg(-1) dry soil and 0 to 50 mg Cu kg(-1) in dry soil and in combinations of both metals. Current year's needles for element analyses, EDS microanalyses, microscopy and glutathione and peroxidase activity analyses were collected from 1-5 seedlings per treatment in September. Seedling biomass in controls, Cu25 and Cu50 differed significantly from the Ni25Cu50 treatment. The root/shoot ratio was highest in the Ni5 treatment, indicating good root growth, though the roots were visibly healthier in the Cu25 treatment than in the Ni5 treatment. At higher Ni levels, the condition of roots deteriorated. The proportion of plasmolysed mesophyll cells was highest in the Ni25 treatment. Copper-treated seedlings did not suffer from Cu stress, because no severe injuries were seen in either the roots or the needles in Cu-exposed seedlings. The needle concentrations of Cu increased only slightly due to treatments. Ni accumulation in needles increased with increasing concentrations in soil. Needles of Cu-treated seedlings had less oxidized glutathione than those of Ni-treated seedlings, but the roots had higher, not significantly, peroxidase activity levels. Light-colored, swollen thylakoids were occasionally observed in the Ni25Cu50 treatment, indicating some interaction between Ni and Cu. Ni seemed to cause more oxidative stress to the seedlings than copper, which was manifested as a decreased GSH level and an increased proportion of GSSG in the Ni treatments. Copper together with nickel strongly decreased root growth, the root/shoot ratio being lowest in the Ni25Cu50 treatment.     

Mobster: accurate detection of mobile element insertions in next generation sequencing data

Mobile elements are major drivers in changing genomic architecture and can cause disease. The detection of mobile elements is hindered due to the low mappability of their highly repetitive sequences. We have developed an algorithm, called Mobster, to detect non-reference mobile element insertions in next generation sequencing data from both whole genome and whole exome studies. Mobster uses discordant read pairs and clipped reads in combination with consensus sequences of known active mobile elements. Mobster has a low false discovery rate and high recall rate for both L1 and Alu elements. Mobster is available at http://sourceforge.net/projects/mobster.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0488-x) contains supplementary material, which is available to authorized users.     

Replicated high-density genetic maps of two great tit populations reveal fine-scale genomic departures from sex-equal recombination rates

Linking variation in quantitative traits to variation in the genome is an important, but challenging task in the study of life-history evolution. Linkage maps provide a valuable tool for the unravelling of such trait−gene associations. Moreover, they give insight into recombination landscapes and between-species karyotype evolution. Here we used genotype data, generated from a 10k single-nucleotide polymorphism (SNP) chip, of over 2000 individuals to produce high-density linkage maps of the great tit (Parus major), a passerine bird that serves as a model species for ecological and evolutionary questions. We created independent maps from two distinct populations: a captive F2-cross from The Netherlands (NL) and a wild population from the United Kingdom (UK). The two maps contained 6554 SNPs in 32 linkage groups, spanning 2010 cM and 1917 cM for the NL and UK populations, respectively, and were similar in size and marker order. Subtle levels of heterochiasmy within and between chromosomes were remarkably consistent between the populations, suggesting that the local departures from sex-equal recombination rates have evolved. This key and surprising result would have been impossible to detect if only one population was mapped. A comparison with zebra finch Taeniopygia guttata, chicken Gallus gallus and the green anole lizard Anolis carolinensis genomes provided further insight into the evolution of avian karyotypes.