Measurement of exhaled hydrogen peroxide from rabbit lungs

Exhaled H2O2 is considered an indicator of lung inflammatory and oxidative stress. Moreover, H2O2 may be involved in signal transduction processes. It is not fully elucidated to what extent (i) H2O2 escapes from the intravascular compartment, and (ii) pulmonary H2O2 generation and nasopharyngeal H2O2 generation contribute to exhaled H2O2. We investigated H2O2 concentrations in breath condensate from isolated buffer-perfused and ventilated rabbit lungs, and from both intubated and spontaneously breathing rabbits with a horseradish peroxidase/2',7'dichlorofluorescin assay. For the perfused lungs, a H2O2 concentration of 58 +/- 19 nM was found. Addition of H2O2 to the buffer fluid resulted in only minute appearance in the exhaled air (<0.001%). Levels of exhaled H2O2 in intubated rabbits and perfused lungs were virtually identical. Nearly ten-fold higher levels were detected in spontaneously breathing rabbits. Decreasing the inspired oxygen concentration from 21% to 1% resulted in a tendency toward decreased H2O2 exhalation in perfused lungs. In contrast, phorbol-12-myristate-13-acetate (PMA) prompted a approximately 4-fold increase in H2O2 exhalation. We conclude that the horseradish peroxidase/2',7'dichlorofluorescin assay is a feasible technique to measure H2O2 in exhaled breath condensate in rabbits. When collecting exhaled air via the tracheal tube, the signal represents pulmonary H2O2 generation with the contribution of the remaining body being negligible.     

The circadian clock as a molecular calendar

There are two dominant environmental oscillators shaping the living conditions of our world: the day-night cycle and the succession of the seasons. Organisms have adapted to these by evolving internal clocks to anticipate these variations. An orchestra of finely tuned peripheral clocks slaved to the master pacemaker of the suprachiasmatic nuclei (SCN) synchronizes the body to the daily 24h cycle. However, this circadian clockwork closely interacts with the seasonal time-teller.

Recent experiments indeed show that photoperiod—the dominant Zeitgeber of the circannual clock—might be deciphered by the organism using the tools of the circadian clock itself. From the SCN, the photoperiodic signal is transferred to the pineal where it is decoded as a varying secretion of melatonin.

Different models have been proposed to explain the mechanism by which the circadian clock measures day-length. Recent work using mutant mice suggests a set of two molecular oscillators tracking dusk and dawn, respectively, thereby translating day-length to the body. However, not every aspect of photoperiodism is covered by this theory and major adjustments will need to be made to establish a widely acceptable uniform model of circadian/circannual timekeeping.     

Genetic diversity and the phylogeography of parthenogenesis: comparing bisexual and thelytokous populations of Nemasoma varicorne (Diplopoda: Nemasomatidae) in Denmark

The millipede, Nemasoma varicorne, represents a textbook example of geographic parthenogenesis with thelytokous populations being distributed north, east, south and west of the distribution of the bisexual ancestor in the deciduous forests of central Europe. We here describe variation in amplified fragment length polymorphisms (AFLP's) in sympatric bisexual and thelytokous populations of N. varicorne in Denmark and compare the relationships of Danish populations with animals from The Czech Republic, England and Poland. Thelytokes from Denmark, England and Poland form a monophyletic cluster that differs from bisexuals from Denmark and Czechia for about 30% of the fragments. A single clone is widely spread over Denmark (34 of 38 localities), with rare clones being detected at four other localities. The phylogenetic pattern implies strongly that thelytoky evolved prior to the post-glacial colonization of northern Europe. This further suggests that the two forms have interacted extensively during this colonization and that the thelytokes have been excluded from older forests by competition with the bisexual forms. Our results further suggest that the success of the thelytokous form, at least in Denmark, is not due to abundant clonal diversity as hypothesized by the frozen niche variation model.     

Molecular cloning and characterization of a cDNA encoding poplar UDP-glucose dehydrogenase,a key gene of hemicellulose/pectin formation

Plant UDP-glucose dehydrogenase (UGDH) is an important enzyme in the formation of hemicellulose and pectin, the components of newly formed cell walls. A cDNA clone (Ugdh) corresponding to UGDH was isolated from a cDNA library prepared from cambial zone of poplar (Populus tremula x tremuloides). Within the 1824-nucleotide (nt)-long clone, an open reading frame encoded a protein of 481 amino acids (aa), with a calculated molecular weight of 53.1 kDa. The derived aa sequence showed 90% and 63% identity with UGDHs from soybean and bovine liver, respectively, and had highly conserved aa motifs believed to be of importance for nt binding and catalytic efficiency. In poplar, the Ugdh corresponds to one or two genes, as found by genomic Southern analysis. The gene was expressed predominantly in differentiating xylem and young leaves, with little expression in the phloem zone of the stem. The expression pattern matched that of UGDH protein, as found by immunoblotting. In leaves, the Ugdh expression was upregulated by a short-term feeding with sucrose, sorbitol and polyethylene glycol, and this effect was to some extent mimicked by light exposure. The data suggest that Ugdh is regulated via an osmoticum-dependent pathway, possibly related to the availability of osmotically active carbohydrate precursors to UDP-glucose, a substrate of UGDH.     

Isolation,crystallisation, and preliminary X-ray analysis of the bovine mitochondrial EF-Tu:GDP and EF-Tu:EF-Ts complexes

Previous studies have shown that when bovine mitochondrial elongation factor Ts (EF-Ts) is expressed in Escherichia coli, it forms a tightly associated complex with E. coli elongation factor Tu (EF-Tu). In contrast to earlier experiments, purification of free mitochondrial EF-Ts was accomplished under nondenaturing conditions since only about 60% of the expressed EF-Ts copurified with E. coli EF-Tu. The bovine mitochondrial EF-Tu:GDP complex, the homologous mitochondrial EF-Tu:EF-Ts complex, and the heterologous E. coli/mitochondrial EF-Tu:EF-Ts complex were isolated and crystallised. The crystals of the EF-Tu:GDP complex diffract to 1.94 A and belong to space group P2(1) with cell parameters a=59.09 A, b=119.78 A, c=128.89 A and beta=96.978 degrees. The crystals of the homologous mitochondrial EF-Tu:EF-Ts complex diffract to 4 A and belong to space group C2 with cell parameters a=157.7 A, b=151.9 A, c=156.9 A, and beta=108.96 degrees.     

A putative DNA-binding domain in the NUCKS protein

We have studied the DNA-binding properties of a NUCKS-derived, synthetic peptide containing an extended GRP motif. This peptide binds to random-sequence DNA, but did not bind preferentially to poly(dA-dT). A synthetic peptide with the same amino acid composition but with a random sequence did not bind to DNA, suggesting that the structure of the DNA-binding domain plays a pivotal role in the interaction with DNA. NMR and graphic modeling were employed to investigate the structure of the synthetic peptide. It was shown that the DNA-binding peptide constituted an alpha helix in phosphate buffer at pH 5.5. Docking results indicated an almost perfect fit for this small, helical peptide into the major groove of DNA with the possibility of four basic residues interacting with the phosphate backbone of DNA. One consensus site for phosphorylation by Cdk1 is located in the N-terminal end of the DNA-binding peptide. Upon phosphorylation of this site, the binding to DNA was completely prohibited. Immunofluorescence experiments showed that NUCKS was located in the nuclei in proliferating cells in interphase of the cell cycle, but was distributed throughout the cytoplasm in mitotic cells.     

Extensive linkage disequilibrium in small human populations in Eurasia

The extent of linkage disequilibrium (LD) was studied in two small food-gathering populations—Evenki and Saami—and two larger food-producing populations—Finns and Swedes—in northern Eurasia. In total, 50 single-nucleotide polymorphisms (SNPs) from five genes were genotyped using real-time pyrophosphate DNA sequencing, whereas 14 microsatellites were genotyped in two X-chromosomal regions. In addition, hypervariable region I of the mtDNA was sequenced to shed light on the demographic history of the populations. The SNP data, as well as the microsatellite data, reveal extensive levels of LD in Evenki and Saami when compared to Finns and Swedes. mtDNA-sequence variation is compatible with constant population size over time in Evenki and Saami but indicates population expansion in Finns and Swedes. Furthermore, the similarity between Finns and Swedes in SNP allele- and haplotype-frequency distributions indicate that these two populations may share a recent common origin. These findings suggest that populations such as the Evenki and the Saami, rather than the Finns, may be particularly suited for the initial coarse mapping of common complex diseases.     

Molecular and functional evidence for electrogenic and electroneutral Na(+)-HCO(3)(-) cotransporters in murine duodenum

Inward Na(+)-HCO(3)(-) cotransport has previously been demonstrated in acidified duodenal epithelial cells, but the identity and localization of the mRNAs and proteins involved have not been determined. The molecular expression and localization of Na(+)-HCO(3)(-) cotransporters (NBCs) were studied by RT-PCR, sequence analysis, and immunohistochemistry. By fluorescence spectroscopy, the intracellular pH (pH(i)) was recorded in suspensions of isolated murine duodenal epithelial cells loaded with 2',7'-bis(2-carboxyethyl)-5(6)-carboxyfluorescein. Proximal duodenal epithelial cells expressed mRNA encoding two electrogenic NBC1 isoforms and the electroneutral NBCn1. Both NBC1 and NBCn1 were localized to the basolateral membrane of proximal duodenal villus cells, whereas the crypt cells did not label with the anti-NBC antibodies. DIDS or removal of extracellular Cl(-) increased pH(i), whereas an acidification was observed on removal of Na(+) or both Na(+) and Cl(-). The effects of inhibitors and ionic dependence of acid/base transporters were consistent with both inward and outward Na(+)-HCO(3)(-) cotransport. Hence, we propose that NBCs are involved in both basolateral electroneutral HCO(3)(-) transport as well as basolateral electrogenic HCO(3)(-) transport in proximal duodenal villus cells.     

Genome organisation and chromatin structure in Escherichia coli

We have analysed the complete sequence of the Escherichia coli K12 isolate MG1655 genome for chromatin-associated protein binding sites, and compared the predicted location of predicted sites with experimental expression data from 'DNA chip' experiments. Of the dozen proteins associated with chromatin in E. coli, only three have been shown to have significant binding preferences: integration host factor (IHF) has the strongest binding site preference, and FIS sites show a weak consensus, and there is no clear consensus site for binding of the H-NS protein. Using hidden Markov models (HMMs), we predict the location of 608 IHF sites, scattered throughout the genome. A subset of the IHF sites associated with repeats tends to be clustered around the origin of replication. We estimate there could be roughly 6000 FIS sites in E. coli, and the sites tend to be localised in two regions flanking the replication termini. We also show that the regions upstream of genes regulated by H-NS are more curved and have a higher AT content than regions upstream of other genes. These regions in general would also be localised near the replication terminus.     

Species richness and abundance of epiphytic Araceae on adjacent floodplain and upland forest in Amazonian Ecuador

Terrestrial plant communities of adjacent upland and floodplain forest of the Amazonian lowland differ from each other in species richness and composition. Epiphytes are generally not considered as being affected by flooding, but we found considerable variation in the communities of epiphytic Araceae of flooded and unflooded forest. Contrary to findings from tree or ground herb communities, no depletion in overall species richness was observed among epiphytic aroids of the floodplains. Abundance and number of epiphytic aroid species per phorophyte were significantly higher than in upland forest, and the species composition varied conspicuously between the two forest types. We suggest that these differences are due to elevated humidity and better soil quality on the floodplains and reject the assumption that flooding has no effect on the epiphytic community.