Mapping the distribution of 3-hydroxy oxylipins in the ascomycetous yeast Saturnispora saitoi

The distribution of 3-hydroxy oxylipins in Saturnispora saitoi was mapped using immunofluorescence microscopy. Fluorescence was observed on aggregating ascospores, indicating the presence of 3-hydroxy oxylipins on the surface or between ascospores. The oxylipin was identified as 3-hydroxy 9:1 using gas chromatography mass spectrometry. Furthermore, ultrastructural studies using scanning and transmission electron microscopy on ascospores revealed a clear equatorial ledge surrounding oval-shaped ascospores.     

Regulation of aldosterone production from zona glomerulosa cells by ANG II and cAMP: evidence for PKA-independent activation of CaMK by cAMP

Aldosterone production in zona glomerulosa (ZG) cells of adrenal glands is regulated by various extracellular stimuli (K(+), ANG II, ACTH) that all converge on two major intracellular signaling pathways: an increase in cAMP production and calcium (Ca(2+)) mobilization. However, molecular events downstream of the increase in intracellular cAMP and Ca(2+) content are controversial and far from being completely resolved. Here, we found that Ca(2+)/calmodulin-dependent protein kinases (CaMKs) play a predominant role in the regulation of aldosterone production stimulated by ANG II, ACTH, and cAMP. The specific CaMK inhibitor KN93 strongly reduced ANG II-, ACTH-, and cAMP-stimulated aldosterone production. In in vitro kinase assays and intact cells, we could show that cAMP-induced activation of CaMK, using the adenylate cyclase activator forskolin or the cAMP-analog Sp-5,6-DCI-cBIMPS (cBIMPS), was not mediated by PKA. Activation of the recently identified cAMP target protein Epac (exchange protein directly activated by cAMP) by 8-pCPT-2'-O-Me-cAMP had no effect on CaMK activity and aldosterone production. Furthermore, we provide evidence that cAMP effects in ZG cells do not involve Ca(2+) or MAPK signaling. Our results suggest that ZG cells, in addition to PKA and Epac/Rap proteins, contain other as yet unidentified cAMP mediator(s) involved in regulating CaMK activity and aldosterone secretion.     

Evaluation of the use of Water Framework Directive typology descriptors, reference sites and spatial scale in macroinvertebrate stream typology

The Rhine ecosystem is highly influenced by anthropogenic stresses from pollution, intensive shipping and increased connectivity with other large European rivers. Canalization of the Rhine resulted in a reduction of heterogeneity to two main biotopes: sandy streambeds and riverbanks consisting of groyne stones. Both biotopes are heavily subjected to biological invasions, affecting the rivers food web structure. The Ponto-Caspian amphipods, Chelicorophium curvispinum and Dikerogammarus villosus, have exerted the highest impact on this food web. The filterfeeding C. curvispinum dominated the Rhine food web on the stones in 1998, swamping the stone substrata with mud. However, in 2001 it decreased in numbers, most likely due to top-down regulation caused by increased parasitic and predatory pressure of other more recently invaded Ponto-Caspian species. D. villosus showed a fast population increase after its invasion and particularly influenced the macroinvertebrate community on the stones by predaceous omnivory. This species seemed to have maintained its predatory level after its population established. Effects of these mass invaders on the macroinvertebrate community of sandy streambeds in the Rhine are unclear. Here, low densities of macroinvertebrates were observed with the Asiatic clam, Corbicula fluminea, as most abundant species. Stable isotope values of food webs from the stones and sand in 2001 were similar. Aquatic macrophytes are nearly absent and the food web is fuelled by phytoplankton and particulate organic matter, originating from riparian vegetation as indicated by similar δ¹³C values. Omnivores, filter-, deposit-, and detritus-feeders are the primary and secondary macroinvertebrate consumers and function as keystone species in transferring energy to higher trophic levels. Invaders comprise 90% of the macroinvertebrate numbers, and can be considered ecosystem engineers determining the functional diversity and food web structure of the Rhine by either bottom-up or top-down regulation.     

Uncertainty in Diatom Assessment: Sampling, Identification and Counting Variation

Despite the widespread application of periphytic diatoms to water quality assessment at a regional level, there is no standard European sampling protocol or associated assessment metrics. Furthermore, relatively little is known about the uncertainty in the results of such assessments. One of the objectives of the European project for the Standardisation of River Classifications (STAR) is to improve and standardise diatom assessment methods. An extensive diatom ring test, together with an audit of the project results, provided a better understanding and quantification of the uncertainty in quality assessment of running waters using diatoms. The variation in multimetric analysis shows that the choice of site and substrate for sampling, the inter-operator differences in diatom taxonomy and the counting techniques are the primary sources of uncertainty. To some extent, this variation also reveals the robustness of specific metrics in relation to the sources of uncertainty. Of the three most common substrate types tested (stone, macrophyte and sediment), macrophytes emerge as the most preferred substrate for diatom sampling when performing multimetric water quality assessment.     

Supramolecular zinc(II)salphen motifs: Reversible dimerization and templated dimeric structures

The formation of a dimeric structure of a nonsymmetric Zn(II)salphen complex is reported. The X-ray molecular structure show the formation of an oxygen-bridged species (2). In addition to this structure, a pyridine-ligated complex and an 1:2 dabco/Zn(II)salphen supramolecular assembly (dabco = diazabicyclo[2.2.2]octane) are presented. Their coordination behavior has been studied and can be correlated with the substitution pattern of the salphen ligand and the donor-strength of the involved axial ligands. The Zn(II)salphen building blocks bind in a cooperative fashion to the dabco template, the second unit being bound 4 times more strongly.     

Dissection of a metastatic gene expression signature into distinct components

Background

Metastasis, the process whereby cancer cells spread, is in part caused by an incompletely understood interplay between cancer cells and the surrounding stroma. Gene expression studies typically analyze samples containing tumor cells and stroma. Samples with less than 50% tumor cells are generally excluded, thereby reducing the number of patients that can benefit from clinically relevant signatures.

Results

For a head-neck squamous cell carcinoma (HNSCC) primary tumor expression signature that predicts the presence of lymph node metastasis, we first show that reduced proportions of tumor cells results in decreased predictive accuracy. To determine the influence of stroma on the predictive signature and to investigate the interaction between tumor cells and the surrounding microenvironment, we used laser capture microdissection to divide the metastatic signature into six distinct components based on tumor versus stroma expression and on association with the metastatic phenotype. A strikingly skewed distribution of metastasis associated genes is revealed.

Conclusion

Dissection of predictive signatures into different components has implications for design of expression signatures and for our understanding of the metastatic process. Compared to primary tumors that have not formed metastases, primary HNSCC tumors that have metastasized are characterized by predominant down-regulation of tumor cell specific genes and exclusive up-regulation of stromal cell specific genes. The skewed distribution agrees with poor signature performance on samples that contain less than 50% tumor cells. Methods for reducing tumor composition bias that lead to greater predictive accuracy and an increase in the types of samples that can be included are presented.     

SynTReN: a generator of synthetic gene expression data for design and analysis of structure learning algorithms

Background  

The development of algorithms to infer the structure of gene regulatory networks based on expression data is an important subject in bioinformatics research. Validation of these algorithms requires benchmark data sets for which the underlying network is known. Since experimental data sets of the appropriate size and design are usually not available, there is a clear need to generate well-characterized synthetic data sets that allow thorough testing of learning algorithms in a fast and reproducible manner.