Genetic effects of supportive stockings on native pikeperch populations in boreal lakes--cases, three different outcomes

The genetic consequences and gene flow of pikeperch (Sander lucioperca) stocking were assessed in three boreal lakes based on admixture model analysis and comparison of the pre- and post-release patterns of genetic variability at 9 DNA microsatellite loci in the recipient populations. In two out of the three cases, the releases of fish from foreign populations caused significant changes in the genetic structure of the recipient population. The largest changes were observed in Lake Ouluj?rvi, where the post-release sample was almost identical to the released Lake Vanajanselk? population, and about 90% of the catch was composed of the released population. The genetic composition of Lake Lohjanj?rvi pikeperch also shifted markedly towards that of the released Lake Vanajanselk? population, and about half of the later catch was of released Vanajanselk? origin. In Lake Vanajanselk?, in contrast, releases of pikeperch from lakes Painio and Averia had only a small impact on the genetic structure of the pikeperch population. These results indicate that the current stocking practices create an effective artificial gene flow that may strongly shape and reduce the genetic differentiation among the remaining native pikeperch populations. A common feature of all three cases was the lack of prior appraisal of the potential genetic and ecological risks in relation to the expected benefits of the release programmes.     

Radiation-induced genomic instability in Caenorhabditis elegans

Currently, the cosmetics industry relies on the results of in vitro genotoxicity tests to assess the safety of chemicals. Although the cytokinesis-block micronucleus (CBMN) test for the detection of cells that have divided once is routinely used and currently accepted by regulatory agencies, it has some limitations. Reconstituted human epidermis (RHE) is widely used in safety assessments because its physiological properties resemble those of the skin, and because it allows testing of substances such as hydrophobic compounds. Thus, the micronucleus test is being adapted for application in RHE-reconstructed tissues. Here we investigated whether two different reconstructed epidermis models (EPI/001 from Straticell, and RHE/S/17 from Skinethic) are suitable for application of the micronucleus test. We found that acetone does not modify micronucleus frequency, cell viability, and model structure, compared with non-treated RHE. Treatment of the EPI/001 model with mitomycin C and vinblastine resulted in a dose-dependent increase of micronucleus frequency as well as a decrease of tissue viability and of binucleated cell rate, while no changes of the epidermal structure were observed. The number of binucleated cells obtained with the RHE/S/17 model was too small to permit micronucleus testing. These results indicate that the proliferative rate of the tissue used is a critical parameter in performing the micronucleus test on a 3D model.     

Extent of industrial plantations on Southeast Asian peatlands in 2010 with analysis of historical expansion and future projections

Tropical peatlands cover over 25 Mha in Southeast Asia and are estimated to contain around 70 Gt of carbon. Peat swamp forest ecosystems are an important part of the region's natural resources supporting unique flora and fauna endemic to Southeast Asia. Over recent years, industrial plantation development on peatland, especially for oil palm cultivation, has created intense debate due to its potentially adverse social and environmental effects. The lack of objective up‐to‐date information on the extent of industrial plantations has complicated quantification of their regional and global environmental consequences, both in terms of loss of forest and biodiversity as well as increases in carbon emissions. Based on visual interpretation of high‐resolution (30 m) satellite images, we find that industrial plantations covered over 3.1 Mha (20%) of the peatlands of Peninsular Malaysia, Sumatra and Borneo in 2010, surpassing the area of Belgium and causing an annual carbon emission from peat decomposition of 230–310 Mt CO_2e. The majority (62%) of the plantations were located on the island of Sumatra, and over two‐thirds (69%) of all industrial plantations were developed for oil palm cultivation, with the remainder mostly being Acacia plantations for paper pulp production. Historical analysis shows strong acceleration of plantation development in recent years: 70% of all industrial plantations have been established since 2000 and only 4% of the current plantation area existed in 1990. ‘Business‐as‐usual’ projections of future conversion rates, based on historical rates over the past two decades, indicate that 6–9 Mha of peatland in insular Southeast Asia may be converted to plantations by the year 2020, unless land use planning policies or markets for products change. This would increase the annual carbon emission to somewhere between 380 and 920 Mt CO_2e by 2020 depending on water management practices and the extent of plantations.     

Ubiquitin Carboxy-Terminal Hydrolase L1 (UCH-L1) is increased in cerebrospinal fluid and plasma of patients after epileptic seizure

ABSTRACT: BACKGROUND: Clinical and experimental studies have demonstrated that seizures can cause molecular and cellular responses resulting in neuronal damage. At present, there are no valid tests for assessing organic damage to the brain associated with seizure. The aim of this study was to investigate cerebrospinal fluid (CSF) and plasma concentrations of Ubiquitin carboxy-terminal hydrolase L1 (UCH-L1), a sensitive indicator of acute injury to brain neurons, in patients with tonic--clonic or partial secondarily generalized seizures due to various etiologies. METHODS: CSF and plasma concentrations of UCH-L1 were assessed in 52 patients within 48 hours after epileptic seizure and in 19 controls using ELISA assays. RESULTS: CSF obtained within 48 hours after seizure or status epilepticus (SE) presented significantly higher levels of UCH-L1 compared to controls (p = 0.008). Plasma UCH-L1 concentrations were negatively correlated with time to sample withdrawal. An analysis conducted using only the first 12 hours post-seizure revealed significant differences between concentrations of UCH-L1 in plasma and controls (p = 0.025). CSF and plasma concentrations were strongly correlated with age in patients with seizure, but not in control patients. Plasma UCH-L1 levels were also significantly higher in patients after recurrent seizures (n = 4) than in those after one or two seizures (p = 0.013 and p = 0.024, respectively). CONCLUSION: Our results suggest that determining levels of neuronal proteins may provide valuable information on the assessment of brain damage following seizure. These data might allow clinicians to make more accurate therapeutic decisions, to identify patients at risk of progression and, ultimately, to provide new opportunities for monitoring therapy and targeted therapeutic interventions.     

Genes involved in systemic and arterial bed dependent atherosclerosis--Tampere Vascular study

Background

Atherosclerosis is a complex disease with hundreds of genes influencing its progression. In addition, the phenotype of the disease varies significantly depending on the arterial bed.

Methodology/Principal Findings

We characterized the genes generally involved in human advanced atherosclerotic (AHA type V–VI) plaques in carotid and femoral arteries as well as aortas from 24 subjects of Tampere Vascular study and compared the results to non-atherosclerotic internal thoracic arteries (n=6) using genome-wide expression array and QRT-PCR. In addition we determined genes that were typical for each arterial plaque studied. To gain a comprehensive insight into the pathologic processes in the plaques we also analyzed pathways and gene sets dysregulated in this disease using gene set enrichment analysis (GSEA). According to the selection criteria used (>3.0 fold change and p-value <0.05), 235 genes were up-regulated and 68 genes down-regulated in the carotid plaques, 242 genes up-regulated and 116 down-regulated in the femoral plaques and 256 genes up-regulated and 49 genes down-regulated in the aortic plaques. Nine genes were found to be specifically induced predominantly in aortic plaques, e.g., lactoferrin, and three genes in femoral plaques, e.g., chondroadherin, whereas no gene was found to be specific for carotid plaques. In pathway analysis, a total of 28 pathways or gene sets were found to be significantly dysregulated in atherosclerotic plaques (false discovery rate [FDR] <0.25).

Conclusions

This study describes comprehensively the gene expression changes that generally prevail in human atherosclerotic plaques. In addition, site specific genes induced only in femoral or aortic plaques were found, reflecting that atherosclerotic process has unique features in different vascular beds.     

Disentangling direct and indirect effects of water table drawdown on above‐ and belowground plant litter decomposition: consequences for accumulation of organic matter in boreal peatlands

Pristine peatlands are carbon (C)‐accumulating wetland ecosystems sustained by a high water table (WT) and consequent anoxia that slows down decomposition. Persistent WT drawdown as a response to climate and/or land‐use change affects decomposition either directly through environmental factors such as increased oxygenation, or indirectly through changes in plant community composition. This study attempts to disentangle the direct and indirect effects of WT drawdown by measuring the relative importance of environmental parameters (WT depth, temperature, soil chemistry) and litter type and/or litter chemical quality on the 2‐year decomposition rates of above‐ and belowground litter (altogether 39 litter types). Consequences for organic matter accumulation were estimated based on the annual litter production. The study sites were chosen to form a three‐stage chronosequence from pristine (undrained) to short‐term (years) and long‐term (decades) WT drawdown conditions at three nutrient regimes. The direct effects of WT drawdown were overruled by the indirect effects through changes in litter type composition and production. Short‐term responses to WT drawdown were small. In long‐term, dramatically increased litter inputs resulted in large accumulation of organic matter in spite of increased decomposition rates. Furthermore, the quality of the accumulated matter greatly changed from that accumulated in pristine conditions. Our results show that the shift in vegetation composition as a response to climate and/or land‐use change is the main factor affecting peatland ecosystem C cycle, and thus dynamic vegetation is a necessity in any model applied for estimating responses of C fluxes to changing environment. We provide possible grouping of litter types into plant functional types that the models could utilize. Furthermore, our results clearly show a drop in soil summer temperature as a response to WT drawdown when an initially open peatland converts into a forest ecosystem, which has not yet been considered in the existing models.     

Genetic Markers Enhance Coronary Risk Prediction in Men: The MORGAM Prospective Cohorts

Background

More accurate coronary heart disease (CHD) prediction, specifically in middle-aged men, is needed to reduce the burden of disease more effectively. We hypothesised that a multilocus genetic risk score could refine CHD prediction beyond classic risk scores and obtain more precise risk estimates using a prospective cohort design.

Methods

Using data from nine prospective European cohorts, including 26,221 men, we selected in a case-cohort setting 4,818 healthy men at baseline, and used Cox proportional hazards models to examine associations between CHD and risk scores based on genetic variants representing 13 genomic regions. Over follow-up (range: 5–18 years), 1,736 incident CHD events occurred. Genetic risk scores were validated in men with at least 10 years of follow-up (632 cases, 1361 non-cases). Genetic risk score 1 (GRS1) combined 11 SNPs and two haplotypes, with effect estimates from previous genome-wide association studies. GRS2 combined 11 SNPs plus 4 SNPs from the haplotypes with coefficients estimated from these prospective cohorts using 10-fold cross-validation. Scores were added to a model adjusted for classic risk factors comprising the Framingham risk score and 10-year risks were derived.

Results

Both scores improved net reclassification (NRI) over the Framingham score (7.5%, p = 0.017 for GRS1, 6.5%, p = 0.044 for GRS2) but GRS2 also improved discrimination (c-index improvement 1.11%, p = 0.048). Subgroup analysis on men aged 50–59 (436 cases, 603 non-cases) improved net reclassification for GRS1 (13.8%) and GRS2 (12.5%). Net reclassification improvement remained significant for both scores when family history of CHD was added to the baseline model for this male subgroup improving prediction of early onset CHD events.

Conclusions

Genetic risk scores add precision to risk estimates for CHD and improve prediction beyond classic risk factors, particularly for middle aged men.     

Estimation of 3D shape, internal density and mechanics of proximal femur by combining bone mineral density images with shape and density templates

Measurement of bone mineral density (BMD) by dual-energy X-ray absorptiometry (DXA) alone is only a moderate predictor of fracture risk. Finite element analysis (FEA) of bone mechanics, based on DXA images, may improve the prediction of fracture risk. We developed a method to estimate the 3D shape and density distribution of the proximal femur, using a 2D BMD image and a femur shape template. Proximal femurs of eighteen human cadavers were imaged using computed tomography and divided into two sets (N = 9 + 9). The template was created from the samples in first set by using 3D generalized Procrustes analysis and thin-plate splines. Subsequently, the template and 2D BMD image were utilized to estimate the shape and internal density distribution of the femurs in the second set. Finally, FEA was conducted based on the original and the estimated bone models to evaluate the effect of geometrical and density distributional errors on the mechanical strength. The volumetric errors induced by the estimation itself were low (<1.4%). In the estimation of bones in the second set, the mean distance difference between the estimated and the original bone surfaces was 0.80 ± 0.19 mm, suggesting feasible estimation of the femoral shape. The mean absolute error in voxel-by-voxel BMD was 120±8 mg cm?3. In FEA, the stiffness of the proximal femur differed by -7±16% between the original and estimated bones. The present method, in comparison with methods used in previous studies, improved the prediction of the geometry, the BMD distribution and the mechanical characteristics of the proximal femur. Potentially, the proposed method could ultimately improve the determination of bone fracture risk.