Tissue slice cultures from humans or rodents: a new tool to evaluate biological effects of heavy ions

The aim of this interdisciplinary project is to establish slice culture preparations from rodents and humans as a new model system for studying effects of X-rays and heavy ions within normal and tumor tissues. The advantage of such slice cultures relies on the conservation of an organotypic environment, the easy treatment and observation by live-imaging microscopy, and the independence from genetic immortalization strategies used to generate cell lines. Rat brains as well as human tumors were cut into 300-μm-thick sections and cultivated in an incubator in a humidified atmosphere at 37°C. This is realized by a membrane-based culture system with a liquid–air interface. With this system, it is possible to keep rodent slices viable for several months. Human brain tumor slices remained vital for at least 21 days. Slices were irradiated with X-rays at the radiation facility of the University Hospital in Frankfurt/Main at doses up to 40 Gy. Heavy ion irradiations were performed at GSI (Darmstadt) with different ions, energies, and doses. The irradiated slices were analyzed by 3D-confocal microscopy following immunostaining for DNA damage, microglia, and proliferation markers. The phosphorylated histone γH2AX proved to be suitable for the detection of ion traversals in this system.     

Functional Annotation,Genome Organization and Phylogeny of the Grapevine (<Emphasis Type="Italic">Vitis vinifera</Emphasis>) Terpene Synthase Gene Family Based on Genome Assembly,FLcDNA Cloning,and Enzyme Assays

Background  

Terpenoids are among the most important constituents of grape flavour and wine bouquet, and serve as useful metabolite markers in viticulture and enology. Based on the initial 8-fold sequencing of a nearly homozygous Pinot noir inbred line, 89 putative terpenoid synthase genes (VvTPS) were predicted by in silico analysis of the grapevine (Vitis vinifera) genome assembly [1]. The finding of this very large VvTPS family, combined with the importance of terpenoid metabolism for the organoleptic properties of grapevine berries and finished wines, prompted a detailed examination of this gene family at the genomic level as well as an investigation into VvTPS biochemical functions.     

Detecting microRNA activity from gene expression data

Background  

MicroRNAs (miRNAs) are non-coding RNAs that regulate gene expression by binding to the messenger RNA (mRNA) of protein coding genes. They control gene expression by either inhibiting translation or inducing mRNA degradation. A number of computational techniques have been developed to identify the targets of miRNAs. In this study we used predicted miRNA-gene interactions to analyse mRNA gene expression microarray data to predict miRNAs associated with particular diseases or conditions.     

Evolutionary distances in the twilight zone--a rational kernel approach

Phylogenetic tree reconstruction is traditionally based on multiple sequence alignments (MSAs) and heavily depends on the validity of this information bottleneck. With increasing sequence divergence, the quality of MSAs decays quickly. Alignment-free methods, on the other hand, are based on abstract string comparisons and avoid potential alignment problems. However, in general they are not biologically motivated and ignore our knowledge about the evolution of sequences. Thus, it is still a major open question how to define an evolutionary distance metric between divergent sequences that makes use of indel information and known substitution models without the need for a multiple alignment. Here we propose a new evolutionary distance metric to close this gap. It uses finite-state transducers to create a biologically motivated similarity score which models substitutions and indels, and does not depend on a multiple sequence alignment. The sequence similarity score is defined in analogy to pairwise alignments and additionally has the positive semi-definite property. We describe its derivation and show in simulation studies and real-world examples that it is more accurate in reconstructing phylogenies than competing methods. The result is a new and accurate way of determining evolutionary distances in and beyond the twilight zone of sequence alignments that is suitable for large datasets.     

The genetic basis of durum wheat germination and seedling growth under osmotic stress

Durum wheat (Triticum turgidum L. var. durum) is mainly produced under rainfed but often sub-optimal moisture conditions in the Mediterranean basin. A set of 114 durum wheat recombinant inbred lines (RILs) developed from the cross of cultivars Omrabi5 × Belikh2 were tested for the ability to tolerate moisture deficiency at the germination and early seedling growth stage. The stress was imposed by exposing the germinating grain to 12 % polyethylene glycol. It induced a measurable reduction in root length, shoot length, and the percentage of normal seedlings. The germination and seedling growth of Belikh2 were more strongly inhibited than those of Omrabi5, and both parents were outperformed by > 50 % of the RILs. A quantitative trait locus (QTL) analysis was carried out by first assembling a linkage map from 265 informative microsatellites. Composite interval mapping revealed nine QTL spread over seven chromosomes. Five of these were associated with coleoptile length, and one of the five explained nearly 29 % of the relevant phenotypic variance. The coleoptile length was significantly correlated with the seedling growth, plant height, and thousand kernel mass derived from field-grown plants of the same RIL population.     

Escherichia coli and enterococci are sensitive and reliable indicators for human,livestock and wildlife faecal pollution in alpine mountainous water resources

Aims: This study evaluated the applicability of standard faecal indicator bacteria (SFIB) for alpine mountainous water resources monitoring. Methods and Results: Escherichia coli, enterococci (ENTC) and Clostridium perfringens were investigated by standard or frequently applied phenotypic and genotypic methods in a broad range of animal and human faecal sources in a large alpine mountainous area. Clostridium perfringens occurred only in human, livestock and carnivorous source groups in relevant average concentrations (log 4·7–7·0 CFU g^?1) but not in herbivorous wildlife sources. Escherichia coli proved to be distributed in all faecal source groups with remarkably balanced average concentrations (log 7·0–8·4 CFU g^?1). Except for single faecal samples from the cattle source group, prevalence rates for ENTC source groups were generally >87% with average concentrations of log 5·3–7·7 CFU g^?1. To test the faecal indication capacity in the environment, faecal prevalence data were comparatively analysed with results from the concurrently performed multi‐parametric microbial source tracking effort on karst spring water quality from the investigated alpine mountainous catchment ( Reischer et al. 2008 ; Environ Microbiol 10:2598–2608). Conclusion: Escherichia coli and enterococci are reliable faecal indicators for alpine mountainous water resources monitoring, although E. coli is the more sensitive one. Clostridium perfringens did not prove to be an indicator of general faecal pollution but is suggested a conservative microbial source tracking marker for anthropogenic faecal influence. Significance and Impact of the Study: Applicability of SFIB is currently hotly debated. This is the first study providing comprehensive information on the applicability of SFIB at alpine mountainous habitats.     

Are environmental factors responsible for geographic variation in the sex ratio of the Greenlandic seed‐bug Nysius groenlandicus?

Until recently nothing indicated an unequal sex ratio in the widespread Greenland seed‐bug Nysius groenlandicus (Zetterstedt) (Heteroptera: Lygaeidae). However, recently populations more or less devoid of males were discovered in high arctic Northeast Greenland. This initiated an inspection of the entire material of the species collected in Greenland and now preserved at the Zoological Museum, University of Copenhagen. It was found that the sex ratio varied significantly among different locations. In most cases females were most abundant, but males were either scarce or absent only in samples from Northeast Greenland, indicating that here the species reproduces asexually. This paper demonstrates that the differing sex distributions can be explained by climatic factors (temperature, precipitation) and that the degree of continentality (distance from the open sea) promotes female‐biased sex ratios.