Statistical evidence for remnants of the primordial code in the acceptor stem of prokaryotic transfer RNA

Summary The specificity of interaction of amino acids with triplets in the acceptor helix stem of tRNA was investigated by means of a statistical analysis of 1400 tRNA sequences. The imprint of a prototypic genetic code at position 3–5 of the acceptor helix was detected, but only for those major amino acids, glycine, alanine, aspartic acid, and valine, that are formed by spark discharges of simple gases in the laboratory. Although remnants of the code at position 3–5 are typical for tRNAs of archaebacteria, eubacteria, and chloroplasts, eukaryotes do not seem to contain this code, and mitochondria take up an intermediary position. A duplication mechanism for the transposition of the original 3–5 code toward its present position in the anticodon stern of tRNA is proposed. From this viewpoint, the mode of evolution of mRNA and functional ribosomes becomes more understandable.Offprint requests to: W. Moller     

Vertical migration behaviour of diatom assemblages of Wadden Sea sediments (Dangast, Germany): a study using cryo-scanning electron microscopy.

The vertical migration behaviour of diatom assemblages inhabiting Wadden Sea sediments near Dangast (Germany) was investigated using cryo-scanning electron microscopy. The diatom assemblages were dominated by small Navicula species. Intertidal sediments which were located at different distances from the high tide level or stayed submerged even throughout low tides were chosen. Samples were prepared and cryofixed in the field. Sampling was restricted to three sets: (i) before the onset of vertical migration, (ii) 3 to 5 h after the onset of vertical migration, and (iii) before the area became flooded again or just prior to dusk. The diatom assemblages inhabiting the different types of sediments did not always show the same response. When the tidal cycle exposed the sediment surfaces during the night cell densities increased in the early morning hours with the onset of light. Later on, although the photon flux density was still increasing, cell densities stayed constant or decreased before the water flooded the areas around noon. In experiments in which the water drained off around noon and the areas became exposed throughout the entire afternoon, cell densities increased even up to dusk when the photon flux density had dropped to values below 20 microM photons m-2 s-1. In an experiment in which the last sampling occurred at 10.15 pm, when the photon flux density had already declined below 10 microM photons m-2 s-1, cell densities had decreased to lower values. This was ca. 1 h before the area was flooded again. Finally, cryo-scanning electron microscopy revealed frequently occurring micro-patches of diatom assemblages which could be differentiated into typical areas of lower and higher cell densities further complicating the pattern of light or water cover induced movements.     

Specific targeting of insect and vertebrate telomeres with pyrrole and imidazole polyamides.

DNA minor groove-binding compounds (polyamides) that target insect and vertebrate telomeric repeats with high specificity were synthesized. Base pair recognition of these polyamides is based on the presence of the heterocyclic amino acids pyrrole and imidazole. One compound (TH52B) interacts uniquely and with excellent specificity (K(d) = 0.12 nM) with two consecutive insect-type telomeric repeats (TTAGG). A related compound, TH59, displays high specificity (K(d) = 0.5 nM) for tandem vertebrate (TTAGGG) and insect telomeric repeats. The high affinity and specificity of these compounds were achieved by bidentate binding of two flexibly linked DNA-binding moieties. Epifluorescence microscopy studies show that fluorescent derivatives of TH52B and TH59 stain insect or vertebrate telomeres of chromosomes and nuclei sharply. Importantly, the telomere-specific polyamide signals of HeLa chromosomes co-localize with the immunofluorescence signals of the telomere-binding protein TRF1. Our results demonstrate that telomere-specific compounds allow rapid estimation of relative telomere length. The insect-specific compound TH52 was shown to be incorporated rapidly into growing Sf9 cells, underlining the potential of these compounds for telomere biology and possibly human medicine.     

Reductive activation of potential antitumor bis(aziridinyl)benzoquinones by xanthine oxidase: competition between oxygen reduction and quinone reduction

The reduction of a series of 2,5-bis(1-aziridinyl)-1,4-benzoquinone (BABQ) derivatives with various 3,6 substituents by the enzyme xanthine oxidase has been studied. The reduction rate has been assayed by measuring the rate of reduction of cytochrome c, which is very efficiently reduced by reduced BABQ species. Under nitrogen, the reduction rate correlated with the quinone reduction potential and steric parameters. Comparing reduction rates under nitrogen and air demonstrates that at BABQ concentrations greater than 25 microM the competition for electrons from xanthine oxidase between oxygen and the BABQ derivative is dominated by the latter. This is also confirmed by the effect of superoxide dismutase (SOD): in the presence of a BABQ derivative, cytochrome c reduction can be totally inhibited by SOD, although the required amount of SOD depends on the redox potential of the quinones. This indicates that SOD causes the equilibrium between semiquinone and superoxide to shift, resulting in a decrease of the semiquinone concentration. It is concluded that reduction by xanthine oxidase is a simple and effective method for reducing aziridinylbenzoquinones.     

A two-dimensional numerical analysis of unsteady flow in the carotid artery bifurcation. A comparison with three-dimensional in-vitro measurements and the influence of minor stenoses

In the present study a two-dimensional finite element model for incompressible Newtonian flow is applicated to the modelling of carotid artery flow. In earlier studies, the numerical model was validated experimentally for several flow configurations. In general the pulsatile flow is characterized by reversed flow regions at the non-divider side walls of both the internal and external carotid arteries. The unsteadiness of the flow is associated with rather complex spatial and temporal velocity distributions and leads to temporal variations of the location and length of the reversed flow regions. As a consequence, pronounced spatial and temporal variations in the wall shear stresses are found. At the non-divider side walls, wall shear stresses are relatively low and exhibits an oscillatory behaviour in space and time. At the divider side walls, wall shear stresses are relatively high and approximately follow the flow rate distribution in time. The aim of this study is not only to present two-dimensional calculations but also to compare the calculated two-dimensional velocity profiles with those from three-dimensional experiments. It is observed that in the common carotid artery and in the proximal parts of the internal and external carotid arteries, the two-dimensional numerical model provides valuable information with respect to the three-dimensional configuration. In the more distal parts of especially the internal carotid artery, deviations are found between the two-dimensional numerical and three-dimensional experimental model. These deviations can mainly be attributed to the neglect of the secondary velocity distribution in the two-dimensional model. In the two-dimensional numerical model the influence of a minor stenosis in the internal carotid artery is hardly distinguishable from a minor geometrical variation without stenosis. Full three-dimensional analyses of the influence of minor stenoses are needed to prove numerically whether in-vivo measurements of the axial velocity distribution are useful in the detection of minor stenoses.     

Transcriptional and biochemical signatures of divergence in natural populations of two species of New Zealand alpine Pachycladon

New Zealand is diverse in alpine and subalpine environments, a consequence of Late Tertiary tectonic and climatic change. However, few studies have sought to evaluate the importance of these environments as abiotic drivers in the diversification of plant species. Of particular interest is the Late Tertiary radiation of Pachycladon, an endemic New Zealand genus of alpine cress. Here we report observations on genome-wide levels of differential expression measured in the habitats of two closely related species of Pachycladon with distinct altitudinal preferences. Using Arabidopsis microarrays, we have identified 310 predominantly hormone- and stress-response genes up-regulated in Pachycladon fastigiata and 324 genes up-regulated in Pachycladon enysii. Expression patterns for glucosinolate biosynthesis and hydrolysis genes (MAM1, MAM-I, MAM-D, AOP2, ESP, ESM1) as well as flavonoid biosynthesis genes (F3'H, FLS, FAH1) were found to be species specific. Predicted differences in flavonoid contents were partly confirmed by high performance liquid chromatography analysis. Differences in glucosinolate profiles and glucosinolate hydrolysis products obtained by high performance liquid chromatography and gas chromatography-mass spectrometry analysis, respectively, also supported inferences from expression analyses. Five glucosinolate chemotypes were matched to known Arabidopsis ecotypes, and the potential adaptive significance of these chemotypes has been discussed. Our findings, in contrast to expectations for evolution of the New Zealand flora, suggest that biotic drivers, such as plant-herbivore interactions, are likely to be as important as abiotic drivers in the diversification of Pachycladon.     

A new polymorphism in the type II deiodinase gene is associated with circulating thyroid hormone parameters

Type II deiodinase (D2) is important in the regulation of local thyroid hormone bioactivity in certain tissues. D2 in skeletal muscle may also play a role in serum triiodothyronine (T(3)) production. In this study, we identified a polymorphism in the 5'-UTR of the D2 gene (D2-ORFa-Gly3Asp). We investigated the association of D2-ORFa-Gly3Asp, and of the previously identified D2-Thr92Ala polymorphism, with serum iodothyronine levels. D2-ORFa-Gly3Asp was identified by sequencing the 5'-UTR of 15 randomly selected individuals. Genotypes for D2-ORFa-Gly3Asp were determined in 156 healthy blood donors (age 46.3 +/- 12.2 yr) and 349 ambulant elderly men (age 77.7 +/- 3.5 yr) and related to serum iodothyronine and TSH levels. D2-ORFa-Asp(3) had an allele frequency of 33.9% in blood bank donors and was associated with serum thyroxine (T(4); Gly/Gly vs. Gly/Asp vs. Asp/Asp = 7.06 +/- 0.14 vs. 6.74 +/- 0.15 vs. 6.29 +/- 0.27 microg/dl, P = 0.01), free T(4) (1.22 +/- 0.02 vs. 1.16 +/- 0.02 vs. 1.06 +/- 0.04 ng/dl, P = 0.001), reverse T(3) (P = 0.01), and T(3)/T(4) ratio (P = 0.002) in a dose-dependent manner, but not with serum T(3) (P = 0.59). In elderly men, D2-ORFa-Asp(3) had a similar frequency but was not associated with serum iodothyronine levels. This new polymorphism in the 5'-UTR of D2 is associated with iodothyronine levels in blood donors but not in elderly men. We hypothesize that this might be explained by the decline in skeletal muscle size during aging, resulting in a relative decrease in the contribution of D2 to serum T(3) production.