Specific and non specific hybridization of oligonucleotide probes on microarrays

Gene expression analysis by means of microarrays is based on the sequence specific binding of mRNA to DNA oligonucleotide probes and its measurement using fluorescent labels. The binding of RNA fragments involving other sequences than the intended target is problematic because it adds a "chemical background" to the signal, which is not related to the expression degree of the target gene. The paper presents a molecular signature of specific and non specific hybridization with potential consequences for gene expression analysis. We analyzed the signal intensities of perfect match (PM) and mismatch (MM) probes of GeneChip microarrays to specify the effect of specific and non specific hybridization. We found that these events give rise to different relations between the PM and MM intensities as function of the middle base of the PMs, namely a triplet- (C>G=T>A>0) and a duplet-like (C=T>0>G=A) pattern of the PM-MM log-intensity difference upon binding of specific and non specific RNA fragments, respectively. The systematic behaviour of the intensity difference can be rationalized on the level of base pairings of DNA/RNA oligonucleotide duplexes in the middle of the probe sequence. Non-specific binding is characterized by the reversal of the central Watson Crick (WC) pairing for each PM/MM probe pair, whereas specific binding refers to the combination of a WC and a self complementary (SC) pairing in PM and MM probes, respectively. The intensity of complementary MM introduces a systematic source of variation which decreases the precision of expression measures based on the MM intensities

On the occurrence of bryophytes and macrolichens in different lowland rain forest types at Mabura Hill, Guyana

A floristic and ecological study of bryophytes and macrolichens in different lowland rain forest types around Mabura Hill, Guyana, South America, yielded 170 species: 52 mosses, 82 liverworts and 36 macrolichens. Lejeuneaceae account for about 30% of the species and are the dominant cryptogamic family of the lowland rain forest. Special attention was paid to the flora of the forest canopy, by using mountaineering techniques. It appeared that 50% of the bryophyte species and 86% of the macrolichens occurred exclusively in the canopy. Dry evergreen 'walaba' forest on white sand is particularly rich in lichens whereas the more humid 'mixed' forest on loamy soil is characterized by a rather rich liverwort flora. More species are exclusive to the mixed forest than to dry evergreen forest due to the 'canopy effect', i.e. the occurrence of xerophytic species in the outer canopy of both dry and humid forests. Furthermore, canopy species have wider vertical distributions on trees in the dry evergreen forest than in the mixed forest, due to the more open canopy foliage of the dry evergreen forest

Constitutional Design: Separation of Financing and Project Decision

We examine the provision of public projects under separate tax and subsidy rules. We find that tax rules separated from project cum subsidy decisions exhibit several advantages when incentive problems of the agenda-setter are taken into account. In particular, tax rules may prevent the proposal of inefficient projects which benefit only a small lobby group. We propose “redistribution efficiency” as a socially desirable property of proposals and find that tax rules always guarantee redistribution efficiency. We show that rules on subsidies combined with discretion regarding taxes always yield socially inferior proposals. Finally, tax rules induce the agenda-setter to look for potential improvements of public projects.constitutional design, provision of public projects, voting, taxes and subsidies

Simultaneous description of bulk and interfacial properties of fluids by the Mie potential

The vapor-liquid equilibrium (VLE) of the Mie potential, where the dispersive exponent is constant (m = 6) while the repulsive exponent n is varied between 9 and 48, is systematically investigated by molecular simulation. For systems with planar vapor-liquid interfaces, long-range correction expressions are derived, so that interfacial and bulk properties can be computed accurately. The present simulation results are found to be consistent with the available body of literature on the Mie fluid which is substantially extended. On the basis of correlations for the considered thermodynamic properties, a multicriteria optimization becomes viable. Thereby, users can adjust the three parameters of the Mie potential to the properties of real fluids, weighting different thermodynamic properties according to their importance for a particular application scenario. In the present work, this is demonstrated for carbon dioxide for which different competing objective functions are studied which describe the accuracy of the model for representing the saturated liquid density, the vapor pressure and the surface tension. It is shown that models can be found which describe simultaneously the saturated liquid density and vapor pressure with good accuracy, and it is discussed to what extent this accuracy can be upheld as the model accuracy for the surface tension is further improved