Mouse Genome-Wide Association Mapping Needs Linkage Analysis to Avoid False-Positive Loci

We carried out genome-wide association (GWA) studies in inbred mouse strains characterized for their lung tumor susceptibility phenotypes (spontaneous or urethane-induced) with panels of 12,959 (13K) or 138,793 (140K) single-nucleotide polymorphisms (SNPs). Above the statistical thresholds, we detected only SNP rs3681853 on Chromosome 5, two SNPs in the pulmonary adenoma susceptibility 1 (Pas1) locus, and SNP rs4174648 on Chromosome 16 for spontaneous tumor incidence, urethane-induced tumor incidence, and urethane-induced tumor multiplicity, respectively, with the 13K SNP panel, but only the Pas1 locus with the 140K SNP panel. Haplotype analysis carried out in the latter panel detected four additional loci. Loci reported in previous GWA studies failed to replicate. Genome-wide genetic linkage analysis in urethane-treated (BALB/c×C3H/He)F2, (BALB/c×SWR/J)F2, and (A/J×C3H/He)F2 mice showed that Pas1, but none of the other loci detected previously or herein by GWA, had a significant effect. The Lasc1 gene, identified by GWA as a functional element (Nat. Genet., 38:888–95, 2006), showed no genetic effects in the two independent intercross mouse populations containing both alleles, nor was it expressed in mouse normal lung or lung tumors. Our results indicate that GWA studies in mouse inbred strains can suffer a high rate of false-positive results and that such an approach should be used in conjunction with classical linkage mapping in genetic crosses.     

Nuclear shield: a multi-enzyme task-force for nucleus protection

Background

In eukaryotic cells the nuclear envelope isolates and protects DNA from molecules that could damage its structure or interfere with its processing. Moreover, selected protection enzymes and vitamins act as efficient guardians against toxic compounds both in the nucleoplasm and in the cytosol. The observation that a cytosolic detoxifying and antioxidant enzyme i.e. glutathione transferase is accumulated in the perinuclear region of the rat hepatocytes suggests that other unrecognized modalities of nuclear protection may exist. Here we show evidence for the existence of a safeguard enzyme machinery formed by an hyper-crowding of cationic enzymes and proteins encompassing the nuclear membrane and promoted by electrostatic interactions.

Methodology/Principal Findings

Electron spectroscopic imaging, zeta potential measurements, isoelectrofocusing, comet assay and mass spectrometry have been used to characterize this surprising structure that is present in the cells of all rat tissues examined (liver, kidney, heart, lung and brain), and that behaves as a “nuclear shield”. In hepatocytes, this hyper-crowding structure is about 300 nm thick, it is mainly formed by cationic enzymes and the local concentration of key protection enzymes, such as glutathione transferase, catalase and glutathione peroxidase is up to seven times higher than in the cytosol. The catalytic activity of these enzymes, when packed in the shield, is not modified and their relative concentrations vary remarkably in different tissues. Removal of this protective shield renders chromosomes more sensitive to damage by oxidative stress. Specific nuclear proteins anchored to the outer nuclear envelope are likely involved in the shield formation and stabilization.

Conclusions/Significance

The characterization of this previously unrecognized nuclear shield in different tissues opens a new interesting scenario for physiological and protection processes in eukaryotic cells. Selection and accumulation of protection enzymes near sensitive targets represents a new safeguard modality which deeply differs from the adaptive response which is based on expression of specific enzymes.     

Effect of the replacement of tropical forests with tree plantations on soil organic carbon levels in the Jomoro district,Ghana

Background and aims

In the Jomoro district in Ghana, tree plantations were the first cause of deforestation in the past, drastically reducing the area occupied by primary forests. The aim of this study was to quantify soil organic carbon (SOC) losses due to a change in land use from primary forest to tree plantations (cocoa, coconut, rubber, oil palm) on the different substrates of the district. Secondary forests and mixed plantations were also included in the study.

Methods

Soils were sampled at different depths up to 100 cm along a series of chronosequences in each of the three substrates (Granite, Lower Birrimian and Tertiary Sands) present in the area.

Results

The highest SOC losses in the 0–30 cm layer were caused by the conversion of primary forests to tree plantations: cocoa ?61 % of the original SOC stock, coconut ?55 %, rubber ?35 % and oil palm 28 %, while mixed plantations and secondary forests showed a loss of 23 % and 21 % of the original SOC stock, respectively. C losses were less apparent from the entire profile (to a depth of 100 cm).

Conclusions

All conversions to tree plantations caused substantial SOC losses, comparable to the conversion of forests to agricultural systems. Secondary forests and mixed plantations were the only sustainable land uses that restricted SOC losses considerably.     

Inflammation and genetics: an insight in the centenarian model

The number of centenarians is growing worldwide. This specific cohort has aroused the attention of scientists worldwide and is considered one of the most valuable models to study the mechanisms involved in the aging process. In fact, they have reached the extreme limits of human life span and, most important of all, they show relatively good health being able to perform their routine daily life. Because they have escaped the common lethal diseases, the role of their genetic background has been brought into focus. In fact, sequence variations, in a variety of pro- or anti-inflammatory cytokine genes, have been found to influence successful ageing and longevity. The key role played by cytokines has been also confirmed in centenarians as we know that inflammation has been related to several pathological burdens (e.g., obesity, atherosclerosis, and diabetes). Successful ageing seems to be related to an optimal functioning of the immune system, pointing out that polymorphisms for the immune system genes, which are involved in the regulation of immune-inflammatory responses, may play a key role in the genetics of ageing. This review provides an update in the field of ageing related to inflammation and genetics.     

Pileated Gibbon Density in Relation to Habitat Characteristics and Post‐logging Forest Recovery

ABSTRACT Although it is known that forest loss and degradation negatively impact most forest‐dwelling primates, such relationships are difficult to quantify because many primates are difficult to survey over large areas. Furthermore, recovery times are also difficult to assess due to a lack of long‐term data. Here, we determined how forest characteristics and habitat disturbance correlate with the abundance of pileated gibbons, Hylobates pileatus. We studied a population in Khao Ang Rue Nai Wildlife Sanctuary in southeastern Thailand, assessed its density using an auditory method combined with distance sampling at 24 randomly placed sample sites. In addition, we determined how simple forest structural characteristics and habitat disturbance correlate with the gibbon abundance. Average gibbon density per site was 1.02 ± 0.16 (SE) groups/km² (range 0–2.74). Bivariate analyses indicated that densities depended on food tree biomass, level of disturbance, evergreen forest cover, time since protection, and distance to the sanctuary boundary. Multiple regression analysis suggested evergreen forest cover and distance to boundary were the most influential factors. Because evergreen forest cover, time since protection, and habitat disturbance are correlated, these results suggest a direct dependence of gibbon densities on mature, undisturbed evergreen forest. While gibbons can persist in disturbed areas if the forest is protected, it appears that recovery to previous densities may take decades. We suggest that this is due to the slow pace of forest regeneration and/or poor recovery potential of gibbons.     

A flexible bioreactor system for constructing in vitro tissue and organ models

To develop in vitro models of cells, tissues and organs we have designed and realized a series of cell culture chambers. Each chamber is purpose designed to simulate a particular feature of the in vivo environment. The bioreactor system is user friendly, and the chambers are easy to produce, sterilize and assemble. In addition they can be connected together to simulate inter-organ or tissue cross-talk. Here we discuss the design philosophy of the bioreactor system and then describe its construction. Preliminary results of validation tests obtained with hepatocytes and endothelial cells are also reported. The results show that endothelial cells are extremely sensitive to small levels of shear stress and that the presence of heterotypic signals from endothelial cells enhances the endogenous metabolic function of hepatocytes.     

Radiocarbon based assessment of soil organic matter contribution to soil respiration in a pine stand of the Campine region, Belgium

The contribution of decomposing soil organic carbon (SOC) to total annual soil respiration (SR) was evaluated by radiocarbon measurements at a Scots pine stand growing on a plaggen soil in the Belgian Campine region. Two approaches were used to estimate the contribution of different C pools to SR. In the first approach, the variations in ¹⁴C content of soil CO₂ efflux were monitored during one year (2003) and compared to the atmospheric and SOC ¹⁴C signatures to determine the contribution of ??fast?? (root respiration and fast decomposing SOC) and ??slow?? cycling C pools to total SR. In the second approach an estimate of the total heterotrophic soil respiration (Rh), comprising the slow cycling C and the heterotrophic part of the fast-cycling C pools, was derived applying a box model based on the amount of the bulk SOC pool and its ¹⁴C-derived mean residence time (MRT). The quantification of the Rh and the decomposition rate of the slow-cycling SOC allows to indirectly determining the contribution of the heterotrophic C that decompose within a year. Measurements of total SR performed in the field allowed assessing the contribution of the different C pools to total soil C efflux. On an annual basis, the fast-cycling C was the main contributor to SR, about 85%, while the contribution of the slow-cycling C (with MRT >1 yr) to total SR was 15%. Total annual Rh was 36% of total SR, which is in the lower range reported for temperate coniferous forests. The comparison of Rh with other estimates for the same site (47?C50% of total SR) suggest a possible underestimation of the C flux from the mineral soil. In fact, the ??very old?? C contained in the plaggen horizon strongly affects the signature of the mostly young C leaving the soil. In conclusion, our results indicate that the contribution of SOC decomposition to total soil CO₂ flux in this forest is less than 40%, and at least half of it comes from organic compounds less than 1 year old.     

The effects of ATP and sodium chloride on the cytochrome c-cardiolipin interaction: the contrasting behavior of the horse heart and yeast proteins

In cells a portion of cytochrome c (cyt c) (15–20%) is tightly bound to cardiolipin (CL), one of the phospholipids constituting the mitochondrial membrane. The CL-bound protein, which has nonnative tertiary structure, altered heme pocket, and disrupted Fe(III)-M80 axial bond, is thought to play a role in the apoptotic process. This has attracted considerable interest in order to clarify the mechanisms governing the cyt c–CL interaction. Herein we have investigated the binding reaction of CL with the c-type cytochromes from horse heart and yeast. Although the two proteins possess a similar tertiary architecture, yeast cyt c displays lower stability and, contrary to the equine protein, it does not bind ATP and lacks pro-apoptotic activity. The study has been performed in the absence and in the presence of ATP and NaCl, two compounds that influence the (horse cyt c)-CL binding process and, thus, the pro-apoptotic activity of the protein. The two proteins behave differently: while CL interaction with horse cyt c is strongly influenced by the two effectors, no effect is observed for yeast cyt c. It is noteworthy that NaCl induces dissociation of the (horse cyt c)–CL complex but has no influence on that of yeast cyt c. The differences found for the two proteins highlight that specific structural factors, such as the different local structure conformation of the regions involved in the interactions with either CL or ATP, can significantly affect the behavior of cyt c in its reaction with liposomes and the subsequent pro-apoptotic action of the protein.