Characterization of a peroxidase from Sphagnum magellanicum

The peroxidase from Sphagnum magellanicum is strongly inhibited by CN^? and N^3? and is rather heat stable. The pH optimum is 5.0. The peroxidase rapidly degrades the common hydroxycinnamic acids and sphagnum acid to non-phenolic products; t-cinnamic acid itself is not attacked. The significance of these reactions is discussed with respect to earlier investigations on the level of cinnamic acids in Sphagnum magellanicum. The peroxidase consists of five acidic and five basic isoenzymes. This band pattern does not change during the colouring of the moss, so that the peroxidase from the green and the red moss is identical.     

Masking repeats while clustering ESTs

A problem in EST clustering is the presence of repeat sequences. To avoid false matches, repeats have to be masked. This can be a time-consuming process, and it depends on available repeat libraries. We present a fast and effective method that aims to eliminate the problems repeats cause in the process of clustering. Unlike traditional methods, repeats are inferred directly from the EST data, we do not rely on any external library of known repeats. This makes the method especially suitable for analysing the ESTs from organisms without good repeat libraries. We demonstrate that the result is very similar to performing standard repeat masking before clustering.     

A multilocus analysis of intraspecific competition and stabilizing selection on a quantitative trait

The equilibrium structure of an additive, diallelic multilocus model of a quantitative trait under frequency- and density-dependent selection is derived. The trait is under stabilizing selection and mediates intraspecific competition as induced, for instance, by differential resource utilization. It is assumed that stabilizing selection is weak, but the strength of competition may be arbitrary relative to it. Density dependence is caused by population regulation, which may be of a very general kind. The number and effects of loci are arbitrary, and stabilizing selection is not necessarily symmetric with respect to the range of phenotypic values. All previously studied models of intraspecific competition for a continuum of resources known to the author reduce to a special case of the present model if overall selection is weak. Therefore, in this case our results are applicable as approximations to all these models. Our central result is the (nearly) complete characterization of the equilibrium and stability structure in terms of all parameters. It is derived under the sole assumption that selection is weak enough relative to recombination to ignore linkage disequilibrium. In particular, necessary and sufficient conditions on the strength of competition relative to stabilizing selection are found that ensure the maintenance of multilocus polymorphism and the occurrence of disruptive selection. In this case, explicit formulas for the number of polymorphic loci at equilibrium, the allele frequencies, the genetic variance, and the strength of disruptive selection are obtained. For two loci, the effects of linkage are investigated analytically; for several loci, they are studied numerically.     

Preterm birth makes the immature intestine sensitive to feeding-induced intestinal atrophy

Preterm birth and formula feeding predispose to small intestinal dysfunction, which may lead to necrotizing enterocolitis (NEC). In piglets, we tested whether the physiological and environmental transitions occurring at birth affect the response of the immature intestine to enteral feeding. Pig fetuses (106 days gestation, term = 115 days) were prepared with esophageal feeding tubes and fed either sow's colostrum (n = 8) or infant formula (n = 7) in utero. After 24 h of oral feeding, the pig fetuses were delivered by cesarean section and their gastrointestinal morphology and function were compared with those of preterm newborn (NB) littermates that were not fed (n = 8) or fed colostrum (n = 7) or formula (n = 13) for 24 h after birth. Before birth, both colostrum and formula feeding resulted in marked increases in intestinal mass, brush-border enzyme activities, and plasma glucagon-like peptide 2 concentrations, to levels similar to those in NB colostrum-fed piglets. In contrast, NB formula-fed piglets showed reduced intestinal growth, decreased brush-border enzyme activities, and intestinal lesions, reflecting NEC. NB formula-fed pigs also showed impaired enterocyte endocytotic function and decreased antioxidative capacity, whereas brush-border enzyme mRNA levels were unaltered, relative to NB colostrum-fed pigs. Our results indicate that the feeding-induced growth and enzyme maturation of the immature intestine are not birth dependent. However, with a suboptimal diet (milk formula), factors related to preterm birth (e.g., microbial colonization and metabolic and endocrine changes) make the immature intestine sensitive to atrophy and development of NEC.     

Physical exercise capacity is associated with coronary and peripheral vascular function in healthy young adults

Short-term exercise training has been shown to improve cardiovascular function, whereas long-term effects of a physically active lifestyle, on coronary artery function in particular, are still not well studied. We explored possible relationships between physical exercise capacity and coronary and peripheral vascular function in healthy young adults. Twenty-nine healthy young male and female volunteers participated in the study. They underwent 1) basic clinical and echocardiographic characterization, 2) coronary flow velocity reserve (CFVR) measurement of the left anterior descending coronary artery (LAD), 3) common carotid artery (CCA) intima-media thickness (IMT) measurement, 4) assessment of CCA stiffness index (SI), 5) forearm flow-mediated vasodilation (FMD), and 6) submaximal exercise test. The calculated weight-adjusted maximal oxygen uptake capacity (Vo(2 max)(c)) was positively correlated to LAD CFVR and inversely correlated to IMT and SI. Also, subjects with high compared with moderate exercise capacity had higher FMD. In addition, subjects with LAD CFVR in the upper median had greater ratios between endothelium-dependent and -independent vasodilation in the forearm and lower SI in CCA. High exercise capacity due to a physically active lifestyle is associated with high coronary and peripheral artery function, indicating an early protective role of physical exercise for cardiovascular health.     

Structural basis for m3G-cap-mediated nuclear import of spliceosomal UsnRNPs by snurportin1

In higher eukaryotes the biogenesis of spliceosomal UsnRNPs involves a nucleocytoplasmic shuttling cycle. After the m7G-cap-dependent export of the snRNAs U1, U2, U4 and U5 to the cytoplasm, each of these snRNAs associates with seven Sm proteins. Subsequently, the m7G-cap is hypermethylated to the 2,2,7-trimethylguanosine (m3G)-cap. The import adaptor snurportin1 recognises the m3G-cap and facilitates the nuclear import of the UsnRNPs by binding to importin-beta. Here we report the crystal structure of the m3G-cap-binding domain of snurportin1 with bound m3GpppG at 2.4 A resolution, revealing a structural similarity to the mRNA-guanyly-transferase. Snurportin1 binds both the hypermethylated cap and the first nucleotide of the RNA in a stacked conformation. This binding mode differs significantly from that of the m7G-cap-binding proteins Cap-binding protein 20 (CBP20), eukaryotic initiation factor 4E (eIF4E) and viral protein 39 (VP39). The specificity of the m3G-cap recognition by snurportin1 was evaluated by fluorescence spectroscopy, demonstrating the importance of a highly solvent exposed tryptophan for the discrimination of m7G-capped RNAs. The critical role of this tryptophan and as well of a tryptophan continuing the RNA base stack was confirmed by nuclear import assays and cap-binding activity tests using several snurportin1 mutants.     

Detecting protein-induced folding of the U4 snRNA kink-turn by single-molecule multiparameter FRET measurements

The kink-turn (k-turn), a new RNA structural motif found in the spliceosome and the ribosome, serves as a specific protein recognition element and as a structural building block. While the structure of the spliceosomal U4 snRNA k-turn/15.5K complex is known from a crystal structure, it is unclear whether the k-turn also exists in this folded conformation in the free U4 snRNA. Thus, we investigated the U4 snRNA k-turn by single-molecule FRET measurements in the absence and presence of the 15.5K protein and its dependence on the Na(+) and Mg(2+) ion concentration. We show that the unfolded U4 snRNA k-turn introduces a kink of 85 degrees +/- 15 degrees in an RNA double helix. While Na(+) and Mg(2+) ions induce this more open conformation of the k-turn, binding of the 15.5K protein was found to induce the tightly kinked conformation in the RNA that increases the kink to 52 degrees +/- 15 degrees . By comparison of the measured FRET distances with a computer-modeled structure, we show that this strong kink is due to the k-turn motif adopting its folded conformation. Thus, in the free U4 snRNA, the k-turn exists only in an unfolded conformation, and its folding is induced by binding of the 15.5K protein.     

An empirical Bayes approach to inferring large-scale gene association networks

MOTIVATION: Genetic networks are often described statistically using graphical models (e.g. Bayesian networks). However, inferring the network structure offers a serious challenge in microarray analysis where the sample size is small compared to the number of considered genes. This renders many standard algorithms for graphical models inapplicable, and inferring genetic networks an 'ill-posed' inverse problem. METHODS: We introduce a novel framework for small-sample inference of graphical models from gene expression data. Specifically, we focus on the so-called graphical Gaussian models (GGMs) that are now frequently used to describe gene association networks and to detect conditionally dependent genes. Our new approach is based on (1) improved (regularized) small-sample point estimates of partial correlation, (2) an exact test of edge inclusion with adaptive estimation of the degree of freedom and (3) a heuristic network search based on false discovery rate multiple testing. Steps (2) and (3) correspond to an empirical Bayes estimate of the network topology. RESULTS: Using computer simulations, we investigate the sensitivity (power) and specificity (true negative rate) of the proposed framework to estimate GGMs from microarray data. This shows that it is possible to recover the true network topology with high accuracy even for small-sample datasets. Subsequently, we analyze gene expression data from a breast cancer tumor study and illustrate our approach by inferring a corresponding large-scale gene association network for 3883 genes.     

Genome diversity and gene haplotypes in the grapevine (<Emphasis Type="Italic">Vitis vinifera</Emphasis> L.), as revealed by single nucleotide polymorphisms

EST (expressed sequence tags) sequencing, SNP (single nucleotide polymorphisms) development and haplotype assessment are powerful tools for the support of marker-assisted selection. The grapevine genome is currently being scavenged in our laboratory using an EST-SNP approach. Nine parental genotypes, used to create five inter- or intra-specific hybrids, have been tested to evaluate the degree of polymorphism between Vitis vinifera, Vitis riparia and a further intraspecific hybrid, measuring their nucleotide diversity. The SNPs were analysed on cDNA sequences of 4 functional classes of genes based on homology with genes present in a public database: sugar metabolism, cell signalling, anthocyanin metabolism and defence related. Primer pairs were deduced and used to amplify corresponding genomic sequences. Almost 12,000 bp of DNA have been scanned revealing differences among genotypes of up to 247 SNPs, with the highest rate of one SNP occurring every 78 bp when clones of different Vitis species are compared. Re-sequencing allowed the definition of haplotypes in the nine genotypes studied and these were confirmed by analysing segregating populations. The efficiency of SSCP, in comparison with re-sequencing, was considered for 25 gene fragments of the same 9 genotypes.these two authors contributed equally to this work     

The crucial role of trehalose and structurally related oligosaccharides in the biosynthesis and transfer of mycolic acids in Corynebacterineae

Trehalose (alpha-D-glucopyranosyl-alpha'-D-glucopyranoside) is essential for the growth of the human pathogen Mycobacterium tuberculosis but not for the viability of the phylogenetically related corynebacteria. To determine the role of trehalose in the physiology of these bacteria, the so-called Corynebacterineae, mutant strains of Corynebacterium glutamicum unable to synthesize trehalose due to the knock-out of the genes of the three pathways of trehalose biosynthesis, were biochemically analyzed. We demonstrated that the synthesis of trehalose under standard conditions is a prerequisite for the production of mycolates, major and structurally important constituents of the cell envelope of Corynebacterineae. Consistently, the trehalose-less cells also lack the cell wall fracture plane that typifies mycolate-containing bacteria. Importantly, however, the mutants were able to synthesize mycolates when grown on glucose, maltose, and maltotriose but not on other carbon sources known to be used for the production of internal glucose phosphate such as fructose, acetate, and pyruvate. The mycoloyl residues synthesized by the mutants grown on alpha-D-glucopyranosyl-containing oligosaccharides were transferred both onto the cell wall and free sugar acceptors. A combination of chemical analytical approaches showed that the newly synthesized glycolipids consisted of 1 mol of mycolate located on carbon 6 of the non reducing glucopyranosyl unit. Additionally, experiments with radioactively labeled trehalose showed that the transfer of mycoloyl residues onto sugars occurs outside the plasma membrane. Finally, and in contradiction to published data, we demonstrated that trehalose 6-phosphate has no impact on mycolate synthesis in vivo.