I/NI-calls for the exclusion of non-informative genes: a highly effective filtering tool for microarray data

MOTIVATION: DNA microarray technology typically generates many measurements of which only a relatively small subset is informative for the interpretation of the experiment. To avoid false positive results, it is therefore critical to select the informative genes from the large noisy data before the actual analysis. Most currently available filtering techniques are supervised and therefore suffer from a potential risk of overfitting. The unsupervised filtering techniques, on the other hand, are either not very efficient or too stringent as they may mix up signal with noise. We propose to use the multiple probes measuring the same target mRNA as repeated measures to quantify the signal-to-noise ratio of that specific probe set. A Bayesian factor analysis with specifically chosen prior settings, which models this probe level information, is providing an objective feature filtering technique, named informative/non-informative calls (I/NI calls). RESULTS: Based on 30 real-life data sets (including various human, rat, mice and Arabidopsis studies) and a spiked-in data set, it is shown that I/NI calls is highly effective, with exclusion rates ranging from 70% to 99%. Consequently, it offers a critical solution to the curse of high-dimensionality in the analysis of microarray data. AVAILABILITY: This filtering approach is publicly available as a function implemented in the R package FARMS (www.bioinf.jku.at/software/farms/farms.html).     

Transcytosis of Streptococcus iniae through skin epithelial barriers: an in vitro study

By constructing a biological model based on in vitro culture of polarized rainbow trout primary skin epithelial cell monolayers, the series of early events that precede Streptococcus iniae infection, particularly colonization and translocation through external barriers, were analyzed. Streptococcus iniae promptly invades skin epithelial cells, but the rapid decline of viable intracellular bacteria points out the limited capability of intracellular survival for this bacterium. Translocation assays, supported by electron microscopy microphotographs, demonstrate that following successful in vitro invasion of skin epithelial cell, the bacterium exists free in the cytoplasm after release from the endosome, and translocates through the skin barrier. Bacterial invasion and transcytosis is not accompanied by apparent cell-line damages or disruption of host cells' tight junctions. It is hypothesized that the phenomenon of epithelial invasion coupled to the rapid translocation through the barrier plays a crucial role in Streptococcus iniae infection.     

QNet: an agglomerative method for the construction of phylogenetic networks from weighted quartets

We present QNet, a method for constructing split networks from weighted quartet trees. QNet can be viewed as a quartet analogue of the distance-based Neighbor-Net (NNet) method for network construction. Just as NNet, QNet works by agglomeratively computing a collection of circular weighted splits of the taxa set which is subsequently represented by a planar split network. To illustrate the applicability of QNet, we apply it to a previously published Salmonella data set. We conclude that QNet can provide a useful alternative to NNet if distance data are not available or a character-based approach is preferred. Moreover, it can be used as an aid for determining when a quartet-based tree-building method may or may not be appropriate for a given data set. QNet is freely available for download.     

Anti-BDCA-4 (neuropilin-1) antibody can suppress virus-induced IFN-alpha production of plasmacytoid dendritic cells

Plasmacytoid dendritic cells (PDC) in human blood are the main source of virus-induced interferon (IFN)-alpha. They exhibit a lineage-negative phenotype but all express BDCA-4, which is homologous to the neuronal receptor neuropilin-1. Specific staining with anti-BDCA-4 antibody is used for positive isolation of PDC from blood by magnetic cells sorting. Here, it is demonstrated that these positively selected PDC showed reduced or completely abolished IFN-alpha release compared to unstained PDC, which were negatively selected by magnetic depletion of lineage-positive blood mononuclear cells. In addition, treatment of these unstained PDC with anti-BDCA-4 mAb also resulted in at least two-fold lower or reduced virus-induced IFN-alpha production. It is shown that the antibody not only affects cell survival or block virus attachment but also reduces IFN-alpha release induced by non-viral CpG oligodeoxynucleotides. In conclusion, data suggest an immunoregulatory role for BDCA-4 on PDC as demonstrated for IFN-alpha response to virus.     

Docking without docking: ISEARCH--prediction of interactions using known interfaces

The increasing number of solved protein structures provides a solid number of interfaces, if protein-protein interactions, domain-domain contacts, and contacts between biological units are taken into account. An interface library gives us the opportunity to identify surface regions on a target molecule that are similar by local structure and residue composition. If both unbound components of a possible protein complex exhibit structural similarities to a known interface, the unbound structures can be superposed onto the known interfaces. The approach is accompanied by two mathematical problems. Protein surfaces have to be quickly screened by thousands of patches, and similarity has to be evaluated by a suitable scoring scheme. The used algorithm (NeedleHaystack) identifies similar patches within minutes. Structurally related sites are recognized even if only parts of the template patches are structurally related to the interface region. A successful prediction of the protein complex depends on a suitable template of the library. However, the performed tests indicate that interaction sites are identified even if the similarity is very low. The approach complements existing ab initio methods and provides valuable results on standard benchmark sets.     

Biodegradation of chlorobenzene under hypoxic and mixed hypoxic-denitrifying conditions

Pseudomonas veronii strain UFZ B549, Acidovorax facilis strain UFZ B530, and a community of indigenous groundwater bacteria, adapted to oxygen limitation, were cultivated on chlorobenzene and its metabolites 2-chloro-cis,cis-muconate and acetate/succinate under hypoxic and denitrifying conditions. Highly sensitive approaches were used to maintain defined low oxygen partial pressures in an oxygen-re-supplying headspace. With low amounts of oxygen available all cultures converted chlorobenzene, though the pure strains accumulated 3-chlorocatechol and 2-chloro-cis,cis-muconate as intermediates. Under strictly anoxic conditions no chlorobenzene transformation was observed, while 2-chloro-cis,cis-muconate, the fission product of oxidative ring cleavage, was readily degraded by the investigated chlorobenzene-degrading cultures at the expense of nitrate as terminal electron acceptor. Hence, we conclude that oxygen is an obligatory reactant for initial activation of chlorobenzene and fission of the aromatic ring, but it can be partially replaced by nitrate in respiration. The tendency to denitrify in the presence of oxygen during growth on chlorobenzene appeared to depend on the oxygen availability and the efficiency to metabolize chlorobenzene under oxygen limitation, which is largely regulated by the activity of the intradiol ring fission dioxygenase. Permanent cultivation of a groundwater consortium under reduced oxygen levels resulted in enrichment of a community almost exclusively composed of members of the β-Proteobacteria and Bacteroidetes. Thus, it is deduced that these strains can still maintain high activities of oxygen-requiring enzymes that allow for efficient CB transformation under hypoxic conditions.     

Genetic differentiation among populations of Cicerbita alpina (L.) Wallroth (asteraceae) in the western Alps

In this study we analyzed the genetic population structure of the hygrophilous tall-herb Cicerbita alpina in the western Alps because this group of mountain plants is underrepresented in the biogeographical literature. AFLP (amplified fragment length polymorphism) fingerprints of 40 samples were analyzed from four populations situated in a transect from the southwestern Alps to the eastern part of the western Alps and one population from the Black Forest outside the Alps. Two genetic groups can be distinguished. The first group (A) comprises the populations from the northern and eastern parts of the western Alps, and the second group (B) comprises the populations from the southwestern Alps and the Black Forest. Group A originates most likely from at least one refugium in the southern piedmont regions of the Alps. This result provides molecular evidence for a humid climate at the southern margin of the Alps during the Würm glaciation. Group B originates presumably from western or northern direction and we discuss two possible scenarios for the colonization of the Alps, i.e. (1) long-distance dispersal from southwestern refugia and (2) colonization from nearby refugia in the western and/or northern Alpine forelands. The study demonstrates that the target species harbours considerable genetic diversity, even on a regional scale, and therefore is a suitable model for phylogeographic research.     

Eco-efficiency

Goal, Scope and Background The eco-efficiency analysis and portfolio is a powerful decision support tool for various strategic and marketing issues. Since its original academic development, the approach has been refined during the last decade and applied to a multitude of projects. BASF, as possibly the most prominent company using and developing this tool, has applied the eco-efficiency approach to more than 300 projects in the last 7 years. One of the greatest difficulties is to cover both dimensions of eco-efficiency (costs or value added and environmental impact) in a comparable manner. This is particularly a challenge for the eco-efficiency analyses of products. Methods In this publication, an important approach and field of application dealing with product decisions based on the combination of Life Cycle Cost (LCC) and Life Cycle Assessment (LCA) is described in detail. Special emphasis is put on the quantitative assessment of the relation of costs and environmental impacts. In conventional LCA an assessment of environmental impact categories is often made by normalization with inhabitant equivalents. This is necessary to be able to compare the different environmental impact categories, because of each different unit. For the proposed eco-efficiency analysis, the costs of products or processes are also normalized with adapted gross domestic product figures. Results and Discussion The ratio between normalized environmental impact categories and normalized costs (R_E,C) is used for the graphical presentation of the results in an eco-efficiency portfolio. For the interpretation of the results of an eco-efficiency analysis, it is important to distinguish ratios R_E,C which are higher than one from ratios lower than one. In the first case, the environmental impact is higher than the cost impact, while the inverse is true in the second case. This is very important for defining which kind of improvement is needed and defining strategic management decisions. The paper shows a statistical evaluation of the R_E,C factor based on the results of different eco-efficiency analyses made by BASF. For industries based on large material flows (e.g. chemicals, steel, metals, agriculture), the R_E,C factor is typically higher than one. Conclusions and Recommendations This contribution shows that LCC and LCA may be combined in a way that they mirror the concept of eco-efficiency. LCAs that do not consider LCC may be of very limited use for company management. For that very reason, corporations should install a data management system that ensures equal information on both sides of the eco-efficiency coin.