Copy number analysis of complement C4A, C4B and C4A silencing mutation by real-time quantitative polymerase chain reaction

Low protein levels and copy number variation (CNV) of the fourth component of human complement (C4A and C4B) have been associated with various diseases. High-throughput methods for analysing C4 CNV are available, but they commonly do not detect the most common C4A mutation, a silencing CT insertion (CTins) leading to low protein levels. We developed a SYBR? Green labelled real-time quantitative polymerase chain reaction (qPCR) with a novel concentration range approach to address C4 CNV and deficiencies due to CTins. This method was validated in three sample sets and applied to over 1600 patient samples. CTins caused C4A deficiency in more than 70% (76/105) of the carriers. Twenty per cent (76/381) of patients with a C4A deficiency would have been erroneously recorded as having none, if the CTins had not been assessed. C4A deficiency was more common in patients than a healthy reference population, (OR?=?1.60, 95%CI?=?1.02-2.52, p?=?0.039). The number of functional C4 genes can be straightforwardly analyzed by real-time qPCR, also with SYBR? Green labelling. Determination of CTins increases the frequency of C4A deficiency and thus helps to elucidate the genotypic versus phenotypic disease associations.     

Genetic diversity in strains of the genus Anabaena isolated from planktonic and benthic habitats of the Gulf of Finland (Baltic Sea)

Late summer cyanobacterial blooms in the Baltic Sea contain Anabaena sp. together with Nodularia spumigena and Aphanizomenon flos-aquae. Although Anabaena is common especially in the Gulf of Finland, very little is known about its genetic diversity. Here we undertook a molecular phylogenetic study of 68 Anabaena strains isolated from the brackish Gulf of Finland. We sequenced the 16S rRNA genes from 54 planktonic and 14 benthic Anabaena strains, and rbcL and rpoC1 genes from a subset of these strains. Phylogenetic trees showed that Anabaena strains, from both planktonic and benthic habitats, were genetically diverse. Although the Anabaena strains were morphologically diverse, in our study only one genetically valid species was found to exist in the plankton. Evolutionary distances between benthic Anabaena strains were greater than between planktonic strains, suggesting that benthic habitats allow for the maintenance of greater genetic diversity than planktonic habitats. A number of novel lineages containing only sequences obtained in this study were compiled in the phylogenetical analyses. Thus, it seemed that novel lineages of the genus Anabaena may be present in the Baltic Sea. Our results demonstrate that the Baltic Sea Anabaena strains show surprisingly high genetic diversity.     

Trends in recent temperature and radial tree growth spanning 2000 years across northwest Eurasia

This paper describes variability in trends of annual tree growth at several locations in the high latitudes of Eurasia, providing a wide regional comparison over a 2000-year period. The study focuses on the nature of local and widespread tree-growth responses to recent warming seen in instrumental observations, available in northern regions for periods ranging from decades to a century. Instrumental temperature data demonstrate differences in seasonal scale of Eurasian warming and the complexity and spatial diversity of tree-growing-season trends in recent decades. A set of long tree-ring chronologies provides empirical evidence of association between inter-annual tree growth and local, primarily summer, temperature variability at each location. These data show no evidence of a recent breakdown in this association as has been found at other high-latitude Northern Hemisphere locations. Using Kendall's concordance, we quantify the time-dependent relationship between growth trends of the long chronologies as a group. This provides strong evidence that the extent of recent widespread warming across northwest Eurasia, with respect to 100- to 200-year trends, is unprecedented in the last 2000 years. An equivalent analysis of simulated temperatures using the HadCM3 model fails to show a similar increase in concordance expected as a consequence of anthropogenic forcing.     

Mountain uplift explains differences in Palaeogene patterns of mammalian evolution and extinction between North America and Europe

Patterns of late Palaeogene mammalian evolution appear to be very different between Eurasia and North America. Around the Eocene–Oligocene (EO) transition global temperatures in the Northern Hemisphere plummet: following this, European mammal faunas undergo a profound extinction event (the Grande Coupure), while in North America they appear to pass through this temperature event unscathed. Here, we investigate the role of surface uplift to environmental change and mammalian evolution through the Palaeogene (66–23 Ma). Palaeogene regional surface uplift in North America caused large-scale reorganization of precipitation patterns, particularly in the continental interior, in accord with our combined stable isotope and ecometric data. Changes in mammalian faunas reflect that these were dry and high-elevation palaeoenvironments. The scenario of Middle to Late Eocene (50–37 Ma) surface uplift, together with decreasing precipitation in higher-altitude regions of western North America, explains the enigma of the apparent lack of the large-scale mammal faunal change around the EO transition that characterized western Europe. We suggest that North American mammalian faunas were already pre-adapted to cooler and drier conditions preceding the EO boundary, resulting from the effects of a protracted history of surface uplift.     

Reconstruction of cell population dynamics using CFSE

Background  

Quantifying cell division and death is central to many studies in the biological sciences. The fluorescent dye CFSE allows the tracking of cell division in vitro and in vivo and provides a rich source of information with which to test models of cell kinetics. Cell division and death have a stochastic component at the single-cell level, and the probabilities of these occurring in any given time interval may also undergo systematic variation at a population level. This gives rise to heterogeneity in proliferating cell populations. Branching processes provide a natural means of describing this behaviour.     

CXCR7 expression disrupts endothelial cell homeostasis and causes ligand-dependent invasion

The homeostatic function of endothelial cells (EC) is critical for a number of physiological processes including vascular integrity, immunity, and wound healing. Indeed, vascular abnormalities resulting from EC dysfunction contribute to the development and spread of malignancies. The alternative SDF-1/CXCL12 receptor CXCR7 is frequently and specifically highly expressed in tumor-associated vessels. In this study, we investigate whether CXCR7 contributes to vascular dysfunction by specifically examining the effect of CXCR7 expression on EC barrier function and motility. We demonstrate that CXCR7 expression in EC results in redistribution of CD31/PECAM-1 and loss of contact inhibition. Moreover, CXCR7+ EC are deficient in barrier formation. We show that CXCR7-mediated motility has no influence on angiogenesis but contributes to another motile process, the invasion of CXCR7+ EC into ligand-rich niches. These results identify CXCR7 as a novel manipulator of EC barrier function via alteration of PECAM-1 homophilic junctions. As such, aberrant expression of CXCR7 in the vasculature has the potential to disrupt vascular homeostasis and could contribute to vascular dysfunction in cancer systems.     

Convergence in the distribution patterns of Europe’s plants and mammals is due to environmental forcing

Aim Our aims were to test: (1) the extent to which vascular plant associations are related in space to mammalian associations, and (2) whether the plant associations are more closely related than the mammalian associations to climate and to a published environmental stratification of Europe. Location Europe, as defined by the following boundaries: 11° W, 32° E, 71° N and 35° N. Methods The analysis is based on presence/absence records of mammal species and plant species with a resolution of 50 km × 50 km. The similarity of the overall spatial structure was tested using a partial Mantel test while controlling for the effect of geographical proximity. To further identify the main spatial components in the datasets, we used k‐means clustering and principal components analysis. The resulting geographical patterns were compared with one another, with climate variables and with the environmental stratification of Europe. Results The clustering of the plant data forms coherent areas that can be interpreted as reflections of floristic regions that are controlled to a large extent by climate and topography. In terms of the correlation between distance matrices, the relationship between plants and mammals is relatively strong. The relationships between mammals and climate, and between plants and climate, are more complex but always statistically significant. There is no evidence that the plant clusters are more closely related than the mammalian clusters to climate, although plant clusters are closer to environmental data than to climate. Main conclusions The clustering patterns of mammals and plants form groups that agree with one another in their spatial extent. The forcing of floristic patterns into coherent entities appears mainly to be caused by climatic variables (temperature, temperature range and rainfall), mediated by elevation differences. The formation of individual plant clusters is also related to species numbers and to local and regional floristic differences. The close correlation between the floristic and faunal patterns suggests that the mammal and plant distributions are controlled by the same environmental variables, although the extent to which the mammals are controlled directly by climate or through the influence of vegetation requires more detailed study.     

The effect of oligonucleotide microarray data pre-processing on the analysis of patient-cohort studies

Background  

Intensity values measured by Affymetrix microarrays have to be both normalized, to be able to compare different microarrays by removing non-biological variation, and summarized, generating the final probe set expression values. Various pre-processing techniques, such as dChip, GCRMA, RMA and MAS have been developed for this purpose. This study assesses the effect of applying different pre-processing methods on the results of analyses of large Affymetrix datasets. By focusing on practical applications of microarray-based research, this study provides insight into the relevance of pre-processing procedures to biology-oriented researchers.