The Old World sparrows (genus Passer) phylogeography and their relative abundance of nuclear mtDNA pseudogenes

The phylogenetic relationships of genus Passer (Old World sparrows) have been studied with species covering their complete world living range. Mitochondrial (mt) cyt b genes and pseudogenes have been analyzed, the latter being strikingly abundant in genus Passer compared with other studied songbirds. The significance of these Passer pseudogenes is presently unclear. The mechanisms by which mt cyt b genes become pseudogenes after nuclear translocation are discussed together with their mode of evolution, i.e., transition/transversion mitochondrial ratio is decreased in the nucleus, as is the constraint for variability at the three codon positions. However, the skewed base composition according to codon position (in 1^st position the percentage is very similar for the four bases, in 2^nd position there are fewer percentage of A and G and more percentage of T, and in 3^rd codon position fewer percentage of G and T and is very rich in A and C) is maintained in the translocated nuclear pseudogenes. Different nuclear internal mechanisms and/or selective pressures must exist for explaining this nuclear/mitochondrial differential DNA base evolutive variability. Also, the phylogenetic usefulness of pseudogenes for defining relationships between closely related lineages is stressed. The analyses suggest that the primitive genus Passer species comes from Africa, the Cape sparrow being the oldest: P. hispaniolensis italiae is more likely conspecific to P. domesticus than to P. hispaniolensis. Also, Passer species are not included within weavers or Estrildinae or Emberizinae, as previously suggested. European and American Emberizinae sparrows are closely related to each other and seem to be the earliest species that radiated among the studied songbirds (all in the Miocene Epoch). Received: 29 November 2000 / Accepted: 22 March 2001     

The 2.15 A crystal structure of CG-16, the developmentally regulated homodimeric chicken galectin

Differential developmental regulation of expression, fine-specificity differences in ligand recognition and disparate capacity for homodimerization are characteristics of the two currently known proto-type chicken galectins. The X-ray crystal structure of the first avian galectin, the homodimeric agglutinin from chicken liver (CG-16), has been solved in the absence of ligand in two crystal forms. Although the arrangement of lectin dimers in the two crystals is different, the structure of the monomers and their association into the extended beta-sandwich that characterises the dimer are virtually identical. The fold establishes a beta-sandwich motif composed of a five-stranded and a six-stranded beta-sheet evocative of proto-type mammalian galectins. The carbohydrate-binding site is occupied by six water molecules that take the place of the sugar in the complex. They help to stabilise in the absence of the ligand the spatial arrangement of the amino acid side-chains involved in sugar recognition. Docking of N-acetyllactosamine into the binding site reveals that three of these water molecules, which are in direct contact with the protein, occupy positions equivalent to the key sugar hydroxyl groups, namely the hydroxyls at positions 4 and 6 of the galactose unit and at position 3 of the N-acetylglucosamine unit. Crystallographic data are fully consistent with the binding features in solution previously derived from chemical mapping with deoxy, fluoro and O-methyl derivatives and laser photo-CIDNP (chemically induced dynamic nuclear polarisation) studies. The possible molecular basis for the monomeric character of the chicken intestinal galectin as well as potential mechanisms of oxidative inactivation by disulphide bridging are evaluated on the basis of the given structural information concerning the CG-16 dimer interface and the cysteine residues, respectively.     

Relationships in subtribe Diocleinae (Leguminosae; Papilionoideae) inferred from internal transcribed spacer sequences from nuclear ribosomal DNA

The complete sequences of nuclear ribosomal DNA (nrDNA) internal transcribed spacer regions (ITS/5.8S) were determined for species belonging to six genera from the subtribe Diocleinae as well as for the anomalous genera Calopogonium and Pachyrhizus. Phylogenetic trees constructed by distance matrix, maximum parsimony and maximum likelihood methods showed that Calopogonium and Pachyrhizus were outside the clade Diocleinae (Canavalia, Camptosema, Cratylia, Dioclea, Cymbosema, and Galactia). This finding supports previous morphological, phytochemical, and molecular evidence that Calopogonium and Pachyrhizus do not belong to the subtribe Diocleinae. Within the true Diocleinae clade, the clustering of genera and species were congruent with morphology-based classifications, suggesting that ITS/5.8S sequences can provide enough informative sites to allow resolution below the genus level. This is the first evidence of the phylogeny of subtribe Diocleinae based on nuclear DNA sequences.     

Modulation of rat liver cytochrome P450 activity by prolonged red wine consumption

Cytochrome P450-dependent oxidation of lauric acid, p-nitrophenol and ethanol by liver microsomal fractions were studied in control rats and in animals given either ethanol, red wine, or alcohol-free red wine for 10 weeks. Ethanol increased the total cytochrome P450 and the isoenzyme 2E1 content, as well as the p-nitrophenol hydroxylation and ethanol oxidation. These effects of ethanol treatment were attenuated by red wine administration. Red wine increased the total antioxidant capacity of plasma, whereas the alcohol-free red wine decreased the cytochrome P450 content and decreased the oxidation of lauric acid, p-nitrophenol and ethanol to values lower than control. It is concluded that red wine administration attenuates the ethanol-induced enhancement in liver microsomal parameters dependent on cytochrome P450 2E1 activity, an affect that seems to be accomplished by the non-alcoholic constituents of red wine known to have antioxidant properties.     

Color vision in the comb frequency domain

In 1982, Horace Barlow considered the question of human trichromacy in the context of information theory: according to the Sampling Theorem, three types of receptors covering the visible spectrum (400-700 nm) might be sufficient to reconstruct the color signal. Although Barlow was led to reject the direct application of the Sampling Theorem to explain color dimensionality, the theoretical framework offers a fresh point of view for analyzing the color system in conjunction with the physical characteristics of natural color signals. This review aims to illustrate that if the strict mathematical reconstruction (as implied by the Sampling Theorem) is replaced by a pragmatic approximation of color signals, then trichromacy, with its subsequent opponent-color process, could be regarded as an optimization of color constancy abilities in the spectral environment of primates. Higher dimension systems (tetrachromacy) found in other species can also serve the purpose of color constancy optimization in environments where color signals exhibit a finer spectral structure.     

Effect of pH and oxalate on hydroquinone-derived hydroxyl radical formation during brown rot wood degradation

The redox cycle of 2,5-dimethoxybenzoquinone (2,5-DMBQ) is proposed as a source of reducing equivalent for the regeneration of Fe2+ and H2O2 in brown rot fungal decay of wood. Oxalate has also been proposed to be the physiological iron reductant. We characterized the effect of pH and oxalate on the 2,5-DMBQ-driven Fenton chemistry and on Fe3+ reduction and oxidation. Hydroxyl radical formation was assessed by lipid peroxidation. We found that hydroquinone (2,5-DMHQ) is very stable in the absence of iron at pH 2 to 4, the pH of degraded wood. 2,5-DMHQ readily reduces Fe3+ at a rate constant of 4.5 x 10(3) M(-1)s(-1) at pH 4.0. Fe2+ is also very stable at a low pH. H2O2 generation results from the autoxidation of the semiquinone radical and was observed only when 2,5-DMHQ was incubated with Fe3+. Consistent with this conclusion, lipid peroxidation occurred only in incubation mixtures containing both 2,5-DMHQ and Fe3+. Catalase and hydroxyl radical scavengers were effective inhibitors of lipid peroxidation, whereas superoxide dismutase caused no inhibition. At a low concentration of oxalate (50 micro M), ferric ion reduction and lipid peroxidation are enhanced. Thus, the enhancement of both ferric ion reduction and lipid peroxidation may be due to oxalate increasing the solubility of the ferric ion. Increasing the oxalate concentration such that the oxalate/ferric ion ratio favored formation of the 2:1 and 3:1 complexes resulted in inhibition of iron reduction and lipid peroxidation. Our results confirm that hydroxyl radical formation occurs via the 2,5-DMBQ redox cycle.     

Mutants of the Lactose Carrier of Escherichia coli Which Show Altered Sugar Recognition Plus a Severe Defect in Sugar Accumulation

Lactose and melibiose are actively accumulated by the wild-type Escherichia coli lactose carrier, which is an integral membrane protein energized by the proton motive force. Mutants of the E. coli lactose carrier were isolated by their ability to grow on minimal plates with succinate plus IPTG in the presence of the toxic lactose analog β-thio-o-nitrophenylgalactoside (TONPG). TONPG-resistant mutants were streaked on melibiose MacConkey indicator plates, and red clones were picked. These melibiose positive mutants were then streaked on lactose MacConkey plates, and white clones were picked. Transport assays indicated that the mutants had altered sugar recognition and a defect in sugar accumulation. The mutants had a poor apparent K _m for both lactose and melibiose in transport. One mutant had almost no ability to take up lactose, but melibiose downhill transport was 58% (V _max ) of normal. All of the mutants accumulated methyl-α-d-galactopyranoside (TMG) to only 8% or less of normal, and two failed to accumulate. Immunoblot analysis of the mutant lactose carrier proteins indicated that loss of sugar transport activity was not due to loss of expression in the membrane. Nucleotide sequencing of the lacY gene from the mutants revealed changes in the following amino acids of the lactose carrier: M23I, W151L, G257D, A295D and G377V. Two of the mutants (G257D and G377V) are novel in that they represent the first amino acids in periplasmic loops to be implicated with changes in sugar recognition. We conclude that the amino acids M23, W151, G257, A295 and G377 of the E. coli lactose carrier play either a direct or an indirect role in sugar recognition and accumulation. Received: 12 October 1999/Revised: 21 December 1999     

Effects of hypoxic preconditioning on the hypoxicreoxygenated atria from fed and fasted rats

Hypoxic preconditioning (PC) was studied using rat atria set up isometrically in 10 mM dextrose medium and paced at 1 Hz, applying three different protocols wherein fed and 24-h fasted rats were used in protocols 1 and 2 and only the fed in protocol 3. In protocol 1, PC was achieved applying a 5 min hypoxia followed by 10 min of reoxygenation before the onset of a 60 min hypoxia and 60 min reoxygenation. In protocol 2 the 5 min and a posterior 45 min hypoxia were applied in the absence of dextrose whereas in the 10 min and 60 min reoxygenation periods dextrose was present. In protocol 3, two cycles of 5 min dextrose-free hypoxic periods were applied before the sustained hypoxia (dextrose-free) and reoxygenation periods (10 min and final 45 min, both in the presence of dextrose). In the control groups of all protocols, the equilibration periods were prolonged to compensate the duration of PC. In the control groups of protocols 1 and 2, the sustained hypoxia evoked greater disturbances of contractility and a smaller post-hypoxic recovery in the fasted than in the fed rat atria. In protocol 1, PC markedly reduced the rise in resting tension and improved the post-hypoxic recovery in the fasted rat atria whereas in the fed rat atria protective effects were small and brief. In protocol 2, PC evoked a small reduction of contracture only in the atria from fasted rats and in protocol 3, PC exacerbated the hypoxic disturbances. These data suggest that PC effects depend both on the severity of the PC stress and the sustained hypoxia; and that PC does not require coronary flow.     

Cu, Pt, and Pd complexes of the 3-deoxy-1,2-bis(thiosemicarbazone) derived from D-glucose

3-Deoxy-D-erythro-hexos-2-ulose bis(thiosemicarbazone) (1) acts as a tetradentate ligand of the N2S2 type which forms stable coordination complexes with metal(II) cations. The Cu(II), Pt(II), and Pd(II) chelates (2, 4, and 6, respectively) of 1 were synthesized and characterized by elemental analysis and NMR spectroscopy. The NMR spectra of the Pt complex (4) showed the coupling of H-1 and C-1, C-2 of the bis(thiosemicarbazone) with 195Pt (33.7% naturally occurring), which supports the structure proposed for the chelate. The complexes 2, 4, and 6 were acetylated to give the corresponding tri-O-acetyl derivatives 3, 5, and 7. Elimination of Cu(II) from 3 with hydrogen sulfide afforded 8, the tri-O-acetyl derivative of 1. Preliminary studies have shown antiviral activity of chelates 2, 4, and 6 against poliovirus type 1.     

Biochemical characterization, cDNA cloning and protein crystallization of aryl-alcohol oxidase from Pleurotus pulmonarius

Aryl-alcohol oxidase (AAO) involved in lignin degradation by Pleurotus pulmonarius has been purified and characterized. The enzyme was produced in glucose-peptone medium and isolated in a sole chromatographic step using Sephacryl S-200. The purified enzyme is an extracellular glycoprotein with 14% N-carbohydrate content and an estimated molecular mass of 70.5 kDa and pI of 3.95. The kinetic studies showed the highest enzyme affinity against p-anisyl alcohol, with constants similar to those of Pleurotus eryngii and Bjerkandera adusta AAO but different from the intracellular AAO described in Phanerochaete chrysosporium, which present the highest activity on m-anisyl alcohol. Simultaneously, the cDNA of P. pulmonarius AAO has been cloned and sequenced. The translation of this sequence consisted of 593 amino acids including a signal peptide of 27 amino acids. The comparison with other alcohol oxidases, 35% amino acid identity with glucose oxidase, showed highly conserved amino acid sequences in N-terminal and C-terminal regions, in spite of differences in substrate specificity. Crystallization of AAO, carried out for the first time using the P. pulmonarius enzyme, will permit to obtain a molecular model for this oxidase and establish some characteristic of its catalytic site and general structure.