The effect of the 3'-OH group on the conformation and binding ability of anhydropyrimidine nucleosides to uridine phosphorylase

2,2'-Anhydro-3'-deoxy-5-ethyluridine, a new pyrimidine nucleoside analog, has been examined in terms of its binding potency to uridine phosphorylase, and its conformation in solution (NMR) was studied. 2,2'-Anhydro-3'-deoxy-5-ethyluridine has a Ki value of 3.4 microM for uridine phosphorylase from rat intestinal mucosa. This value is approximately one order of magnitude lower than the Km for uridine (22 microM), the natural substrate. The presence of the 3'-OH group (in the ribo-configuration) on pyrimidine nucleoside analogs may not be considered a prerequisite for the binding to uridine phosphorylase; however, it enhances the binding in the case of flexible ligands cooperating in the process of conformation change toward a more favorable enzyme-ligand interaction. The presence of the 3'-OH group in pyrimidine nucleosides seems to be essential if the molecule is to become a substrate.     

A graphical method for detecting recombination in phylogenetic data sets

Current phylogenetic tree reconstruction methods assume that there is a single underlying tree topology for all sites along the sequence. The presence of mosaic sequences due to recombination violates this assumption and will cause phylogenetic methods to give misleading results due to the imposition of a single tree topology on all sites. The detection of mosaic sequences caused by recombination is therefore an important first step in phylogenetic analysis. A graphical method for the detection of recombination, based on the least squares method of phylogenetic estimation, is presented here. This method locates putative recombination breakpoints by moving a window along the sequence. The performance of the method is assessed by simulation and by its application to a real data set.      

bilbo, a non-LTR retrotransposon of Drosophila subobscura: a clue to the evolution of LINE-like elements in Drosophila

We used the repetitive character of transposable elements to isolate a non-LTR retrotransposon in Drosophila subobscura. bilbo, as we have called it, has homology to TRIM and LOA elements. Sequence analysis showed a 5' untranslated region (UTR), an open reading frame (ORF) with no RNA-binding domains, a downstream ORF that had structural homology to that of the I factor, and, finally, a 3' UTR which ended in several 5-nt repeats. The results of our phylogenetic and structural analyses shed light on the evolution of Drosophila non-LTR retrotransposons and support the hypothesis that an ancestor of these elements was structurally complex.      

Variation of physico-chemical parameters along a river transect through the Okavango Delta,Botswana

The Okavango Delta depends on water quantity and quality to sustain its ecosystem services. Whereas many studies have been carried out on its hydrology, few have been done on water quality in the delta. Water pH, electrical conductivity (EC), dissolved oxygen (DO), turbidity, total suspended solids (TSS) and dissolved organic carbon (DOC) were monitored at 10 sites along the Okavango–Boro–Thamalakane–Lake Ngami system almost fortnightly from June 2008 to June 2010. Water quality in the delta was generally good, despite high evapotranspiration rates which would normally produce very saline waters. Electrical conductivity and water temperature increased with distance from Mohembo to Lake Ngami, the former most likely due to evapoconcentration. In contrast, pH, DO, turbidity and TSS decreased with distance from Mohembo to Boro at the lower end of the seasonal floodplain, before increasing again to Lake Ngami. Dissolved oxygen and TSS most likely declined due to biological uptake and particle sedimentation, respectively. Strong and significant relationships were observed between TSS and turbidity and between DOC and EC, indicating that turbidity and EC could be useful proxies for routine estimations of TSS and DOC, respectively, in the delta.     

Macroinvertebrates as bioindicators of water quality in the Mkondoa River,Tanzania, in an agricultural area

The suitability of using macroinvertebrates as bioindicators of stream water quality was tested in the Mkondoa River in an agricultural area at Kilosa, using the rapid bioassessment protocol. The family biotic index (FBI) showed marked variation in water quality along the stream from values ranging from 4.1 to 5.0 in the upstream reaches, indicating good water quality, 5.3 to 5.5 in the mid-reaches and 6.0 to 6.5 in the lower reaches. The water quality index (WQI) indicated that water quality was fair (77 ± 0.98) in the upstream reach of the Mkondoa, marginal (55 ± 0.86) in the midstream reach and poor (33 ± 0.45) in the downstream reach. There were significant relationships between biological oxygen demand and dissolved oxygen and the occurrence of specific taxa, mainly Chironomus and Caenis. Significant changes in macroinvertebrate abundance were mostly related to changes in water quality. As in other parts of the world, macroinvertebrate communities proved to be good biological indicators of water quality and they should be used as bioindicators in long-term monitoring of this river.     

Possible role of a regulatory gene product upon the myo-inositol-1-phosphate synthase production in Neurospora crassa

The regulatory effect of inositol on inositol-1-phosphate synthase in Neurospora crassa strains was studied. Inositol represses enzyme production in the cultures of the wild type and that of the thermosensitive inositol-requiring mutant grown at 22°C. Enzyme activity as well as the quantity of enzyme protein decreased sharply in both strains by increasing concentrations of inositol in the medium. Inositol-requiring strains used in our experiments can be divided into two groups. The first group produces a protein related immunologically to inositol phosphate synthase, but which is enzymatically inactive. The synthesis of this defective enzyme was also repressed by inositol. In the second group, this protein was found to be completely lacking, in both the thermosensitive mutant grown at 37°C, and in a strain requiring inositol due to a reciprocal translocation. The thermostability and the cross immunoelectrophoresis of the enzyme suggest that in the case of the thermosensitive inositol-requiring mutant, the mutation did not occur in the structural gene of the enzyme, but its regulation was probably affected.     

Conformation of the synthetic DNA poly(amino2dA-dT) duplex in high-salt and aqueous alcohol solutions.

It has previously been demonstrated by other workers that the duplex of a synthetic DNA poly(amino2dA-dT) undergoes a salt-induced conformational isomerization. We show in the present work using circular dichroism that the same isomerization is induced in poly(amino2dA-dT) by various alcohols. The isomerization was originally identified as the B-to-Z and then B-to-A conformational transition of DNA but we demonstrate that the high-salt or alcohol conformation of poly (amino2dA-dT) is the non Z-DNA zig-zag double helix we have previously observed with poly(dA-dT) and called X-DNA. X-DNA is a cesium cation specific conformation of poly(dA-dT) while no similar cation specificity is observed with poly(amino2dA-dT). Thus it appears that the extra amino group attached to A and cesium cations make the same thing; they probably dehydrate the double helix minor groove and relieve its conformational variability. Poly(amino2dA-dT) is exceptionally stable in X-DNA and conditions inducing it are mild, which opens the door to assess its molecular structure.     

Demonstration of myo-inositol-1-phosphate synthase and its assumed defective variant in various Neurospora crassa strains by immunological methods.

Immunological experiments were performed to demonstrate myo-inositol-1-phosphate synthase (EC 5.5.1.4) and its assumed defective variant in various Neurospora crassa stains. An enzymatically inactive protein fraction was isolated from the inl-mutant by the same procedure as that of the enzyme. It consisted of several components by gel electrophoresis, and produced a positive immune reaction demonstrated by immunodiffusion using immune sera produced against the enzyme. Using immunodisc gel electrophoresis it produced an immunoprecipitate of slightly lower mobility than the enzyme itself. Similarly, positive immune reactions were obtained with the enzyme using immune sera produced against the protein fraction isolated from the inl- mutant. Enzyme activity was demonstrated both in a strain transformed by wild-type DNA and in a spontaneous revertant. The enzymes were subsequently isolated from both strains, and some properties were compared with those of the wild-type enzyme. The specific activities were lower but the Michaelis constants were nearly the same. The immunodisc gel electrophoretic patterns of these enzymes were similar to that of the protein fraction from the inositol requiring mutant.     

Patterns of beta diversity in Europe: the role of climate,land cover and distance across scales

Aim We test the prediction that beta diversity (species turnover) and the decay of community similarity with distance depend on spatial resolution (grain). We also study whether patterns of beta diversity are related to variability in climate, land cover or geographic distance and how the independent effects of these variables depend on the spatial grain of the data. Location Europe, Great Britain, Finland and Catalonia. Methods We used data on European birds, plants, butterflies, amphibians and reptiles, and data on British plants, Catalonian birds and Finnish butterflies. We fitted two or three nested grids of varying resolutions to each of these datasets. For each grid we calculated differences in climate, differences in land‐cover composition (CORINE) and beta diversity (β_sim, β_Jaccard) between all pairs of grid cells. In a separate analysis we looked specifically at pairs of adjacent grid cells (the first distance class). We then used variation partitioning to identify the magnitude of independent statistical associations (i.e. independent effects in the statistical sense) of climate, land cover and geographic distance with spatial patterns of beta diversity. Results Beta diversity between grid cells at any given distance decreased with increasing grain. Geographic distance was always the most important predictor of beta diversity for all pairwise comparisons at the extent of Europe. Climate and land cover had weaker but distinct and grain‐dependent effects. Climate was more important at relatively coarse grains, whereas land‐cover effects were stronger at finer grains. In the country‐wide analyses, climate and land cover were more important than geographic distance. Climatic and land‐cover models performed poorly and showed no systematic grain dependence for beta diversity between adjacent grid cells. Main conclusions We found that relationships between geographic distance and beta diversity, as well as the environmental correlates of beta diversity, are systematically grain dependent. The strong independent effect of distance indicates that, contrary to the current belief, a substantial fraction of species are missing from areas with a suitable environment. Moreover, the effects of geographic distance (at continental extents) and land cover (at fine grains) indicate that any species distribution modelling should take both environment and dispersal limitation into account.