A metabolomics perspective of human brain tumours

During the past decade or so, a wealth of information about metabolites in various human brain tumour preparations (cultured cells, tissue specimens, tumours in vivo) has been accumulated by global profiling tools. Such holistic approaches to cellular biochemistry have been termed metabolomics. Inherent and specific metabolic profiles of major brain tumour cell types, as determined by proton nuclear magnetic resonance spectroscopy ((1)H MRS), have also been used to define metabolite phenotypes in tumours in vivo. This minireview examines the recent advances in the field of human brain tumour metabolomics research, including advances in MRS and mass spectrometry technologies, and data analysis.     

Neuronostatin, a novel peptide encoded by somatostatin gene, regulates cardiac contractile function and cardiomyocyte survival

Neuronostatin, a recently discovered peptide encoded by somatostatin gene, is involved in regulation of neuronal function, blood pressure, food intake, and drinking behavior. However, the biological effects of neuronostatin on cardiac myocytes are not known, and the intracellular signaling mechanisms induced by neuronostatin remain unidentified. We analyzed the effect of neuronostatin in isolated perfused rat hearts and in cultured primary cardiomyocytes. Neuronostatin infusion alone had no effect on left ventricular (LV) contractile function or on isoprenaline- or preload-induced increase in cardiac contractility. However, infusion of neuronostatin significantly decreased the positive inotropic response to endothelin-1 (ET-1). This was associated with an increase in phosphorylation of p38 mitogen-activated protein kinase and c-Jun N-terminal kinase (JNK). Treatment of both neonatal and adult cardiomyocytes with neuronostatin resulted in reduced cardiomyocyte viability. Inhibition of JNK further increased the neuronostatin-induced cell death. We conclude that neuronostatin regulates cardiac contractile function and cardiomyocyte survival. Receptors for neuronostatin need to be identified to further characterize the biological functions of the peptide.     

Context dependency and metacommunity structuring in boreal headwater streams

We studied the relative importance of spatial and environmental factors as determinants of algal, bryophyte, and macroinvertebrate metacommunities in two boreal drainage basins differing in spatial extent. We used eigenfunction spatial analysis to model the spatial relationships among sites and distance‐based redundancy analysis to partition the variability in biotic communities between the spatial filters generated through spatial eigenfunction analysis and the environmental factors measured in the field. In the smaller study area, each metacommunity was structured mostly by environmental factors. This was evidenced by the fact that either the pure environmental effect was significant or environmental factors were strongly spatially structured. In the larger study area, only pure environmental effects were significant. These findings suggest that the environmental control prevails in boreal headwater streams. However, our findings also suggest that the specific details of the community‐environment and community–space relationships are dependent on the focal organism group and drainage basin.     

Does the interpolation accuracy of species distribution models come at the expense of transferability?

Model transferability (extrapolative accuracy) is one important feature in species distribution models, required in several ecological and conservation biological applications. This study uses 10 modelling techniques and nationwide data on both (1) species distribution of birds, butterflies, and plants and (2) climate and land cover in Finland to investigate whether good interpolative prediction accuracy for models comes at the expense of transferability – i.e. markedly worse performance in new areas. Models’ interpolation and extrapolation performance was primarily assessed using AUC (the area under the curve of a receiver characteristic plot) and Kappa statistics, with supplementary comparisons examining model sensitivity and specificity values. Our AUC and Kappa results show that extrapolation to new areas is a greater challenge for all included modelling techniques than simple filling of gaps in a well‐sampled area, but there are also differences among the techniques in the degree of transferability. Among the machine‐learning modelling techniques, MAXENT, generalized boosting methods (GBM), and artificial neural networks (ANN) showed good transferability while the performance of GARP and random forest (RF) decreased notably in extrapolation. Among the regression‐based methods, generalized additive models (GAM) and generalized linear models (GLM) showed good transferability. A desirable combination of good prediction accuracy and good transferability was evident for three modelling techniques: MAXENT, GBM, and GAM. However, examination of model sensitivity and specificity revealed that model types may differ in their tendencies to either increased over‐prediction of presences or absences in extrapolation, and some of the methods show contrasting changes in sensitivity vs specificity (e.g. ANN and GARP). Among the three species groups, the best transferability was seen with birds, followed closely by butterflies, whereas reliable extrapolation for plant species distribution models appears to be a major challenge at least at this scale. Overall, detailed knowledge of the behaviour of different techniques in various study settings and with different species groups is of utmost importance in predictive modelling.     

Effect of habitat area and isolation on plant trait distribution in European forests and grasslands

A number of studies show contrasting results in how plant species with specific life‐history strategies respond to fragmentation, but a general analysis on whether traits affect plant species occurrences in relation to habitat area and isolation has not been performed. We used published data from forests and grasslands in north‐central Europe to analyse if there are general patterns of sensitivity to isolation and dependency of area for species using three traits: life‐span, clonality, and seed weight. We show that a larger share of all forest species was affected by habitat isolation and area as compared to grassland species. Persistence‐related traits, life‐span and clonality, were associated to habitat area and the dispersal and recruitment related trait, seed weight, to isolation in both forest and grassland patches. Occurrence of clonal plant species decreased with habitat area, opposite to non‐clonal plant species, and long‐lived plant species decreased with grassland area. The directions of these responses partly challenge some earlier views, suggesting that further decrease in habitat area will lead to a change in plant species community composition, towards relatively fewer clonal and long‐lived plants with large seeds in small forest patches and fewer clonal plants with small seeds in small grassland patches. It is likely that this altered community has been reached in many fragmented European landscapes consisting of small and isolated natural and semi‐natural patches, where many non‐clonal and short‐lived species have already disappeared. Our study based on a large‐scale dataset reveals general and useful insights concerning area and isolation effects on plant species composition that can improve the outcome of conservation and restoration efforts of plant communities in rural landscapes.     

NF1 gene expression in mouse fracture healing and in experimental rat pseudarthrosis.

Neurofibromatosis type 1 (NF1) is an inherited disease with an incidence of about 1:3000 worldwide. Approximately half of all patients with NF1 present osseous manifestations, which can vary from mild to severely debilitating changes such as congenital pseudarthrosis. In the present study, fracture healing of mouse tibia was followed and specimens were collected 5, 9, 14, and 22 days postoperatively. Experimental pseudarthrosis of rat was followed up to 15 weeks postoperatively. In situ hybridization and immunohistochemistry were used to demonstrate expression of NF1 tumor suppressor and phosphorylated p44/42 mitogen-activated protein kinase (MAPK), an indicator of the Ras-MAPK pathway. The results showed that ossified callus was formed in mouse fracture 22 days after the operation. The final outcome of rat pseudarthrosis was detected 9 weeks after the operation, presenting abundant cartilaginous callus at the pseudarthrosis. NF1 gene expression was noted in the maturing and in the hypertrophic cartilages during normal mouse fracture healing, and in rat pseudarthrosis. Phosphorylated p44/42 MAPK was detected in a subpopulation of the hypertrophic chondrocytes in both models. Furthermore, positive labeling for NF1 mRNA and protein was detected in endothelium in both the pseudarthrosis and in the fracture. In conclusion, NF1 gene expression and function are needed for normal fracture healing, possibly restraining excessive Ras-MAPK pathway activation.     

Invasion phylogeography of the Ponto-Caspian crustacean Limnomysis benedeni dispersing across Europe

Aim  Limnomysis benedeni Czerniavsky, 1882 is a mysid crustacean native to the Ponto-Caspian (Black and Caspian Sea) rivers and estuaries, and has recently spread across Europe through intentional and unintentional introductions. We explored the structuring of genetic variation in native and non-native populations with an aim to trace the sources of the invasions, and to infer whether the spread has occurred through a single or multiple invasion waves.
Location  Native estuaries in the Ponto-Caspian basin (Volga, Don, Dnieper, Dniester, Danube) and the recently colonized range along the Danube–Rhine river systems and Lithuania.
Methods  A fragment of the mitochondrial COI gene was sequenced to assess genetic affinities and diversity in native and recently established populations.
Results  The genetic diversity in the native regions is organized into several strongly diverged haplotype groups or lineages, partly allopatric, partly sympatric. All these lineages have also spread beyond the native range. Even the recent rapid dispersal across Europe along the Danube–Rhine system towards the North Sea basin involved several lineages from the Danube delta sector. The structuring of genetic diversity among invaded sites suggests multiple invasion events to the Danube–Rhine drainage. This contrasts with data from some other Ponto-Caspian species, where a single haplotype seems to have occupied most invaded areas. There is no evidence that intentionally stocked reservoirs in the Baltic Sea basin would have contributed to further unintentional spread of L. benedeni.
Main conclusions  Limnomysis benedeni is spreading across Europe using the southern invasion corridor. The invasion most likely involved several waves from differentiated sources in the native Danube delta area.     

Predicting spring frost sensitivity by bud development and temperature sum in Norway spruce seedlings

Nurseries would benefit greatly if frost hardiness (FH) of seedlings could be predicted by some environmental variable or by bud development in spring. We investigated the FH of 1-year-old Norway spruce (Picea abies (L.) Karst.) seedlings of local origin. The seedlings were stored frozen until incubated in the growth chamber at six different temperature sums (TSs) (0, 55, 88, 142, 185 and 240 d.d., >5°C) from mid-February to mid-March. FH of the buds, stems and previous year needles was assessed on three occasions. When the TS was 88 d.d. or less, buds exhibited only microscopic signs of development, even when seedlings tolerated temperatures below −10°C. As TS increased, primordial needles and primordial stems of buds grew while FH weakened, especially in previous year needles. When the TS was at least 142 d.d., all plant parts were frost hardy to approximately −6°C. Monitoring TS and bud development can help predict FH of Norway spruce seedlings in spring. However, more studies with seedlings of different ages and from multiple locations are necessary to appreciate the generality of our results.