Chromosome X-Wide Association Study Identifies Loci for Fasting Insulin and Height and Evidence for Incomplete Dosage Compensation

The X chromosome (chrX) represents one potential source for the “missing heritability” for complex phenotypes, which thus far has remained underanalyzed in genome-wide association studies (GWAS). Here we demonstrate the benefits of including chrX in GWAS by assessing the contribution of 404,862 chrX SNPs to levels of twelve commonly studied cardiometabolic and anthropometric traits in 19,697 Finnish and Swedish individuals with replication data on 5,032 additional Finns. By using a linear mixed model, we estimate that on average 2.6% of the additive genetic variance in these twelve traits is attributable to chrX, this being in proportion to the number of SNPs in the chromosome. In a chrX-wide association analysis, we identify three novel loci: two for height (rs182838724 near FGF16/ATRX/MAGT1, joint P-value = 2.71×10⁻⁹, and rs1751138 near ITM2A, P-value = 3.03×10⁻¹⁰) and one for fasting insulin (rs139163435 in Xq23, P-value = 5.18×10⁻⁹). Further, we find that effect sizes for variants near ITM2A, a gene implicated in cartilage development, show evidence for a lack of dosage compensation. This observation is further supported by a sex-difference in ITM2A expression in whole blood (P-value = 0.00251), and is also in agreement with a previous report showing ITM2A escapes from X chromosome inactivation (XCI) in the majority of women. Hence, our results show one of the first links between phenotypic variation in a population sample and an XCI-escaping locus and pinpoint ITM2A as a potential contributor to the sexual dimorphism in height. In conclusion, our study provides a clear motivation for including chrX in large-scale genetic studies of complex diseases and traits.     

Sediment resuspension: rescue or downfall of a thermally stratified eutrophic lake?

The aim of this study was to estimate the effect of sediment resuspension, a common phenomenon in many lakes, on the phosphorus budget of a eutrophicated lake. We used two different approaches, mass balance calculations and spatially comprehensive resuspension measurements, to determine the level of phosphorus loading from which rehabilitation action is started in a dimictic north temperate lake. The effect of resuspension was assumed to be significant, since it often is a governing process for cycling of material in lakes. Internal loading was multifold to that of external loading as determined by the budget calculation. Spatially comprehensive sedimentation and resuspension measurements were necessary, since deep site versus spatially comprehensive measurements had a marked difference in their results. Resuspension of P slightly exceeded the internal loading assessed by budget calculations and thereby proved its significance as a governing in-lake process that influences P cycling strongly. The shallow areas were of importance, since most of the total P load originated from there. The fate of P after resuspension depends on the retention capacity of resuspended particles in addition to prevailing biological and physico-chemical conditions. Therefore, sediment resuspension can either strengthen or diminish internal nutrient load and the processes of the shallow zones are of importance.     

Influence of seasonal time constraints on growth and development of common frog tadpoles: a photoperiod experiment

Organisms living in seasonal environments are often limited by the time available to complete their development. Especially individuals in northern populations may face severe time constraints in their need of completing development before the end of the growth season. Larval amphibians have been widely used in studies of phenotypic plasticity. However, their responses to changes in photoperiod, the main seasonal cue in many organisms, are unknown. In a laboratory experiment, we studied whether common frog (Rana temporaria) tadpoles originating from two populations (separated latitudinally by 1600 km) adjust their growth and development according to the progress of the season by using photoperiodic cues, and whether these responses are temperature dependent. We hypothesised that if frogs use photoperiod as a cue, they should increase growth and development rates as a response to photoperiodic treatments mimicking progressing season. Although our predictions were not verified in either of the populations, photoperiod manipulations had effects on larval life history in both populations. When exposed to progressing season treatments and high temperature, tadpoles from the southern population ceased feeding, which led to delayed metamorphosis and increased mortality. In the northern population, age at metamorphosis was unaffected by the photoperiod treatments, but growth rate until metamorphosis and metamorphic size were slightly larger in the treatments with shorter (increasing or decreasing) day length. Irrespective of photoperiod treatments, growth and development rates, size at metamorphosis and food consumption were higher in the northern as compared to the southern population. These results indicate that in contrast to several insect species, the critical life history decisions in amphibian larvae may not be strongly influenced by photoperiodic cues, but different populations seem to differ in this respect. However, the strong temperature×photoperiod interactions in several traits in the southern population suggest that the role of photoperiodic cues may be affected by other environmental factors, although the ecological significance of these differences remains unclear.     

Combined effect of repetitive work and cold on muscle function and fatigue.

This study compared the effect of repetitive work in thermoneutral and cold conditions on forearm muscle electromyogram (EMG) and fatigue. We hypothesize that cold and repetitive work together cause higher EMG activity and fatigue than repetitive work only, thus creating a higher risk for overuse injuries. Eight men performed six 20-min work bouts at 25 degrees C (W-25) and at 5 degrees C while exposed to systemic (C-5) and local cooling (LC-5). The work was wrist flexion-extension exercise at 10% maximal voluntary contraction. The EMG activity of the forearm flexors and extensors was higher during C-5 (31 and 30%, respectively) and LC-5 (25 and 28%, respectively) than during W-25 (P < 0.05). On the basis of fatigue index (calculated from changes in maximal flexor force and flexor EMG activity), the fatigue in the forearm flexors at the end of W-25 was 15%. The corresponding values at the end of C-5 and LC-5 were 37% (P < 0.05 in relation to W-25) and 20%, respectively. Thus repetitive work in the cold causes higher EMG activity and fatigue than repetitive work in thermoneutral conditions.     

High degree of genetic differentiation in marine three‐spined sticklebacks (Gasterosteus aculeatus)

Populations of widespread marine organisms are typically characterized by a low degree of genetic differentiation in neutral genetic markers, but much less is known about differentiation in genes whose functional roles are associated with specific selection regimes. To uncover possible adaptive population divergence and heterogeneous genomic differentiation in marine three‐spined sticklebacks (Gasterosteus aculeatus), we used a candidate gene‐based genome‐scan approach to analyse variability in 138 microsatellite loci located within/close to (<6 kb) functionally important genes in samples collected from ten geographic locations. The degree of genetic differentiation in markers classified as neutral or under balancing selection—as determined with several outlier detection methods—was low (F_ST = 0.033 or 0.011, respectively), whereas average F_ST for directionally selected markers was significantly higher (F_ST = 0.097). Clustering analyses provided support for genomic and geographic heterogeneity in selection: six genetic clusters were identified based on allele frequency differences in the directionally selected loci, whereas four were identified with the neutral loci. Allelic variation in several loci exhibited significant associations with environmental variables, supporting the conjecture that temperature and salinity, but not optic conditions, are important drivers of adaptive divergence among populations. In general, these results suggest that in spite of the high degree of physical connectivity and gene flow as inferred from neutral marker genes, marine stickleback populations are strongly genetically structured in loci associated with functionally relevant genes.     

The influence of landscape structure on occurrence, abundance and genetic diversity of the common frog, Rana temporaria

Human‐caused habitat destruction and modification constitute one of the largest threats to population persistence and biodiversity, and are also suspected to be the major cause behind the global decline of amphibian populations. We assessed the potential role of agriculture‐related habitat fragmentation on population size and genetic variability in the common frog (Rana temporaria) by recording the occurrence, population density and genetic diversity in three geographically disparate regions in Sweden – each containing landscapes of high and low agricultural activity – and related these to landscape variables extracted from digital maps. We found a highly significant region‐by‐landscape interaction in occurrence, population density and genetic diversity revealing a reversed response to agriculture from south to north: while the effects of agriculture on R. temporaria populations were negative in the south, there were no effects in the central region, whereas positive effects were observed in the north. Spatial autocorrelation analyses of genetic data revealed that populations in high agricultural activity areas were more isolated than populations in low activity areas both in the southern and central regions of Sweden. Landscape diversity showed a strong positive correlation with both density and occurrence of frogs in Sweden as a whole, as well as in the southern region. Also, negative effects of roads and positive effects of ditches on genetic diversity were found in the south. Overall, these results suggest clear but regionally opposite effects of habitat structure on the population size and genetic diversity of amphibian populations. This means that the management strategy aiming to maximize the size and genetic diversity of local common frog populations, and perhaps also those of other amphibian populations, should account for regional differences in existing land‐use patterns.     

Heterogeneity of cellular proliferation within transitional cell carcinoma: correlation of protein kinase C alpha/betaI expression and activity.

A total of 18 histological samples containing both transitional cell carcinoma (TCC) and normal urothelial epithelium were analyzed for protein kinase C (PKC)-alpha and -betaI expression, and for their phosphorylated substrates. The results showed an increased expression of PKC-alpha in 13 out of 18 samples and -betaI in 11 out of 18 TCC samples when compared with normal urothelium. In addition, 11 out of 18 of the TCC tumors displayed heterogeneous expression of the PKC isoenzymes, with different levels of immunosignal in different areas of the tumor. Within the same sample, areas of highest PKC isoenzyme expression also showed highest classical PKC activity, as estimated by immunodetection of phosphorylated forms of PKC substrates. The areas of highest expression of PKC-alpha and/or -betaI isoenzymes showed also the highest number of cells positive for Ki67, an indicator of proliferation. Immunofluorescence and Western blotting demonstrated that in cultured TCC cells, PKC-alpha was located in the cytoplasm, whereas PKC-betaI was located primarily in the nucleus as a 65-kDa fragment and in the cytoplasm as a full-size 79-kDa protein. Our results indicate that increased expression of PKC-alpha and -betaI leads to increased total classical PKC kinase activity and suggest that increased activity of the isoenzymes plays a role in accelerated growth of TCC. Furthermore, these results suggest that even in carcinoma tissue, PKC expression and activity are under strict control.