Higher-level snake phylogeny inferred from mitochondrial DNA sequences of 12S rRNA and 16S rRNA genes

Portions of two mitochondrial genes (12S and 16S ribosomal RNA) were sequenced to determine the phylogenetic relationships among the major clades of snakes. Thirty-six species, representing nearly all extant families, were examined and compared with sequences of a tuatara and three families of lizards. Snakes were found to constitute a monophyletic group (confidence probability [CP] = 96%), with the scolecophidians (blind snakes) as the most basal lineages (CP = 99%). This finding supports the hypothesis that snakes underwent a subterranean period early in their evolution. Caenophidians (advanced snakes), excluding Acrochordus, were found to be monophyletic (CP = 99%). Among the caenophidians, viperids were monophyletic (CP = 98%) and formed the sister group to the elapids plus colubrids (CP = 94%). Within the viperids, two monophyletic groups were identified: true vipers (CP = 98%) and pit vipers plus Azemiops (CP = 99%). The elapids plus Atractaspis formed a monophyletic clade (CP = 99%). Within the paraphyletic Colubridae, the largely Holarctic Colubrinae was found to be a monophyletic assemblage (CP = 98%), and the Xenodontinae was found to be polyphyletic (CP = 91%). Monophyly of the henophidians (primitive snakes) was neither supported nor rejected because of the weak resolution of relationships among those taxa, except for the clustering of Calabaria with a uropeltid, Rhinophis (CP = 94%).      

The inf luence of advection on Calanus near Svalbard: statistical relations between salinity, temperature and copepod abundance

We quantify statistical relationships between hydrography andabundance of Calanus spp. in the Arctic–Atlantic transitionzone around Svalbard (78–82°N) during early autumn.The Atlantic species C. finmarchicus was more abundant in warmerand more saline waters, as expected from its distributionalcore area. Conversely, the Arctic species C. hyperboreus wasmore abundant in colder and fresher waters. However, the Arcticspecies C. glacialis showed opposing relationships with hydrographyin shallow compared with deep regions. In shallow waters, thenumbers of C. glacialis decreased with temperature and salinityas expected, while somewhat surprisingly the opposite trendwas found in deep locations. Sub-surface hydrography between50–150 m was in most cases a better predictor for Calanusspp. abundance than near-surface conditions, the former generallyexplaining up to 50% of the variability in abundance of eachspecies. Despite finding significant relationships between hydrographicproperties and the abundance of each of the three Calanus species,we did not detect significant relationships between the totalCalanus biomass and temperature.     

Neisseria gonorrhoeae O-linked pilin glycosylation: functional analyses define both the biosynthetic pathway and glycan structure

Neisseria gonorrhoeae expresses an O-linked protein glycosylation pathway that targets PilE, the major pilin subunit protein of the Type IV pilus colonization factor. Efforts to define glycan structure and thus the functions of pilin glycosylation (Pgl) components at the molecular level have been hindered by the lack of sensitive methodologies. Here, we utilized a 'top-down' mass spectrometric approach to characterize glycan status using intact pilin protein from isogenic mutants. These structural data enabled us to directly infer the function of six components required for pilin glycosylation and to define the glycan repertoire of strain N400. Additionally, we found that the N. gonorrhoeae pilin glycan is O-acetylated, and identified an enzyme essential for this unique modification. We also identified the N. gonorrhoeae pilin oligosaccharyltransferase using bioinformatics and confirmed its role in pilin glycosylation by directed mutagenesis. Finally, we examined the effects of expressing the PglA glycosyltransferase from the Campylobacter jejuni N-linked glycosylation system that adds N-acetylgalactosamine onto undecaprenylpyrophosphate-linked bacillosamine. The results indicate that the C. jejuni and N. gonorrhoeae pathways can interact in the synthesis of O-linked di- and trisaccharides, and therefore provide the first experimental evidence that biosynthesis of the N. gonorrhoeae pilin glycan involves a lipid-linked oligosaccharide precursor. Together, these findings underpin more detailed studies of pilin glycosylation biology in both N. gonorrhoeae and N. meningitidis, and demonstrate how components of bacterial O- and N-linked pathways can be combined in novel glycoengineering strategies.     

Analysis of an N-terminal deletion in subunit <Emphasis Type="Italic">a</Emphasis> of the <Emphasis Type="Italic">Escherichia coli</Emphasis> ATP synthase

Subunit a is a membrane-bound stator subunit of the ATP synthase and is essential for proton translocation. The N-terminus of subunit a in E. coli is localized to the periplasm, and contains a sequence motif that is conserved among some bacteria. Previous work has identified mutations in this region that impair enzyme activity. Here, an internal deletion was constructed in subunit a in which residues 6–20 were replaced by a single lysine residue, and this mutant was unable to grow on succinate minimal medium. Membrane vesicles prepared from this mutant lacked ATP synthesis and ATP-driven proton translocation, even though immunoblots showed a significant level of subunit a. Similar results were obtained after purification and reconstitution of the mutant ATP synthase into liposomes. The location of subunit a with respect to its neighboring subunits b and c was probed by introducing cysteine substitutions that were known to promote cross-linking: a_L207C + c_I55C, a_L121C + b_N4C, and a_T107C + b_V18C. The last pair was unable to form cross-links in the background of the deletion mutant. The results indicate that loss of the N-terminal region of subunit a does not generally disrupt its structure, but does alter interactions with subunit b.     

Using the satellite-derived NDVI to assess ecological responses to environmental change

Assessing how environmental changes affect the distribution and dynamics of vegetation and animal populations is becoming increasingly important for terrestrial ecologists to enable better predictions of the effects of global warming, biodiversity reduction or habitat degradation. The ability to predict ecological responses has often been hampered by our rather limited understanding of trophic interactions. Indeed, it has proven difficult to discern direct and indirect effects of environmental change on animal populations owing to limited information about vegetation at large temporal and spatial scales. The rapidly increasing use of the Normalized Difference Vegetation Index (NDVI) in ecological studies has recently changed this situation. Here, we review the use of the NDVI in recent ecological studies and outline its possible key role in future research of environmental change in an ecosystem context.     

Inhibition of mitochondrial NADH:ubiquinone oxidoreductase by ethoxyformic anhydride

The NADH:ubiquinone, but not the NADH:ferricyanide, reductase activity of mitochondrial complex I (NADH:ubiquinone oxidoreductase) is inhibited by incubation of the enzyme at pH 6.0 and 0 degree C with ethoxyformic anhydride (EFA), and the inhibition is partially reversed by subsequent incubation of EFA-treated complex I with hydroxylamine. These results and spectral changes of EFA-treated complex I in the u.v. region are consistent with modification of essential histidyl or tyrosyl residues between the primary NADH dehydrogenase and the site of ubiquinone reduction. Treatment of complex I with EFA in the presence of high concentrations of Seconal or Demerol did not protect against EFA inactivation, suggesting that the site of EFA modification may not be the same as the inhibiton sites of Seconal and Demerol. However, the presence of NADH during incubation of complex I with EFA greatly enhanced the inhibition rate, indicating that the reduced conformation of complex I is more susceptible to attack by EFA.     

Generation of C3a anaphylatoxin from human C3 by human mast cell tryptase

Tryptase, the dominant neutral protease of human pulmonary mast cell secretory granules, has the capacity in vitro to generate C3a anaphylatoxin from purified human C3. Only the alpha-chain of C3 is cleaved, and major fragments with apparent m.w. of 105,000, 39,500, 34,000, 29,000, and 9000 are detected by sodium dodecyl sulfate (SDS) polyacrylamide gel electrophoresis under reducing conditions. Fragments of 34,000 and 9000 m.w. are detected without reduction. A portion of the 9000 m.w. protein corresponds to C3a by virtue of its co-migration in SDS polyacrylamide gels with purified C3a and with trypsin-generated C3a, by its detection in a radioimmunoassay for C3a, and by its contractile activity on the guinea pig ileum bioassay. In the presence of heparin, another component of the mast cell secretory granule, the rate of appearance and the distribution of C3 cleavage fragments as assessed in SDS polyacrylamide gels are not appreciably changed with the exception that no C3a material can be detected in the SDS polyacrylamide gels or by radioimmunoassay and bioassay of the unresolved reaction mixture. Enhanced catabolism of authentic C3a by tryptase occurs in the presence of heparin and by analogy when C3a is generated from C3 by tryptase in the presence of heparin. Whereas tryptase secreted by activated human mast cells may generate C3a, a potentially important additional mediator of immediate hypersensitivity events, the concomitant release of heparin may serve to down-regulate C3a irrespective of its mechanism of generation.