Biogeography of Southern Ocean prokaryotes: a comparison of the Indian and Pacific sectors

We investigated the Southern Ocean (SO) prokaryote community structure via zero-radius operational taxonomic unit (zOTU) libraries generated from 16S rRNA gene sequencing of 223 full water column profiles. Samples reveal the prokaryote diversity trend between discrete water masses across multiple depths and latitudes in Indian (71–99°E, summer) and Pacific (170–174°W, autumn-winter) sectors of the SO. At higher taxonomic levels (phylum-family) we observed water masses to harbour distinct communities across both sectors, but observed sectorial variations at lower taxonomic levels (genus-zOTU) and relative abundance shifts for key taxa such as Flavobacteria, SAR324/Marinimicrobia, Nitrosopumilus and Nitrosopelagicus at both epi- and bathy-abyssopelagic water masses. Common surface bacteria were abundant in several deep-water masses and vice-versa suggesting connectivity between surface and deep-water microbial assemblages. Bacteria from same-sector Antarctic Bottom Water samples showed patchy, high beta-diversity which did not correlate well with measured environmental parameters or geographical distance. Unconventional depth distribution patterns were observed for key archaeal groups: Crenarchaeota was found across all depths in the water column and persistent high relative abundances of common epipelagic archaeon Nitrosopelagicus was observed in deep-water masses. Our findings reveal substantial regional variability of SO prokaryote assemblages that we argue should be considered in wide-scale SO ecosystem microbial modelling.     

Automated gas chromatographic assay for amlodipine in plasma and gingival crevicular fluid

This paper describes an automated capillary gas chromatographic method for the determination of amlodipine in plasma, and in sub-microlitre volumes of gingival crevicular fluid (GCF), in order to assess if amlodipine is present in GCF under conditions of gingival overgrowth, as has been shown for nifedipine, another dihydropyridine drug. Liquid-liquid extraction followed by derivatisation was employed to isolate amlodipine and render it suitable for gas chromatography. Amlodipine was analysed in plasma and GCF of four patients undergoing amlodipine therapy for cardiovascular disorders, three of whom had significant gingival overgrowth. Amlodipine was detected in the plasma of all patients and in massive concentrations in the GCG of those patients with overgrowth, 23- to 290-fold greater than in their plasma. Like nifedipine, amlodipine sequestration into GCF appears to be linked with gingival overgrowth.     

EPR spin trapping and 2-deoxyribose degradation studies of the effect of pyridoxal isonicotinoyl hydrazone (PIH) on *OH formation by the Fenton reaction

The search for effective iron chelating agents was primarily driven by the need to treat iron-loading refractory anemias such as beta-thalassemia major. However, there is a potential for therapeutic use of iron chelators in non-iron overload conditions. Iron can, under appropriate conditions, catalyze the production of toxic oxygen radicals which have been implicated in numerous pathologies and, hence, iron chelators may be useful as inhibitors of free radical-mediated tissue damage. We have developed the orally effective iron chelator pyridoxal isonicotinoyl hydrazone (PIH) and demonstrated that it inhibits iron-mediated oxyradical formation and their effects (e.g. 2-deoxyribose oxidative degradation, lipid peroxidation and plasmid DNA breaks). In this study we further characterized the mechanism of the antioxidant action of PIH and some of its analogs against *OH formation from the Fenton reaction. Using electron paramagnetic resonance (EPR) with 5, 5-dimethyl-1-pyrroline-N-oxide (DMPO) as a spin trap for *OH we showed that PIH and salicylaldehyde isonicotinoyl hydrazone (SIH) inhibited Fe(II)-dependent production of *OH from H2O2. Moreover, PIH protected 2-deoxyribose against oxidative degradation induced by Fe(II) and H2O2. The protective effect of PIH against both DMPO hydroxylation and 2-deoxyribose degradation was inversely proportional to Fe(II) concentration. However, PIH did not change the primary products of the Fenton reaction as indicated by EPR experiments on *OH-mediated ethanol radical formation. Furthermore, PIH dramatically enhanced the rate of Fe(II) oxidation to Fe(III) in the presence of oxygen, suggesting that PIH decreases the concentration of Fe(II) available for the Fenton reaction. These results suggest that PIH and SIH deserve further investigation as inhibitors of free-radical mediated tissue damage.     

Pattern of respiration by intact inflorescences of the thermogenic arum lily Philodendron selloum

Inflorescences of the neotropical arum lily, Philodendron selloum, are strongly thermogenic for 2 d during anthesis. Continuous measurements of spadix temperature (Ts) and rate of oxygen consumption (VO2) were made outdoors in whole inflorescences attached to the plants. Some inflorescences were exposed to uncontrolled ambient temperature (Ta) while others were enclosed in clear water-jackets that produced nearly constant ambient conditions. A repeatable, diphasic pattern of heat production appeared, most clearly in water-jacketed inflorescences, and it comprised a short peak phase at sunset followed by a plateau phase that lasted until the following sunset. Regulation of Ta occurred in both phases, but at different levels. Peak phase Ta was regulated in the region of 38-42C, but plateau phase Ta was usually in the range of 25-36C. Both VO2 and total heat produced throughout anthesis increased at lower Ta. The data imply that the short peak phase is related to the enhancement of odour production that attracts a single species of large scarabaeid beetle in its native Brazil, and regulation of maximum Ta may prevent overheating. Thermoregulation in the long plateau phase produces equable temperatures inside the inflorescence that may facilitate the resident beetles' activities as a direct energetic reward.     

Characterisation of the binding interaction between poly(L-lysine) and DNA using the fluorescamine assay in the preparation of non-viral gene delivery vectors

A major factor limiting the development of non-viral gene delivery systems is the poor characterisation of polyelectrolyte complexes formed between cationic polymers and DNA. The present study uses the fluorescamine reagent to improve characterisation of poly(L-lysine) (pLL)/DNA complexes post-modified with a multivalent hydrophilic polymer by determining the availability of free amino groups. The results show that the fluorescamine reagent can be used to monitor the self-assembly reaction between pLL and DNA and the degree of surface modification of the resultant complexes with a hydrophilic polymer. This experimental approach should enable the preparation of fully defined complexes whose properties can be better related to their biological activity.     

Promiscuous protein biotinylation by Escherichia coli biotin protein ligase

Biotin protein ligases (BPLs) are enzymes of extraordinary specificity. BirA, the BPL of Escherichia coli biotinylates only a single cellular protein. We report a mutant BirA that attaches biotin to a large number of cellular proteins in vivo and to bovine serum albumin, chloramphenicol acetyltransferase, immunoglobin heavy and light chains, and RNAse A in vitro. The mutant BirA also self biotinylates in vivo and in vitro. The wild type BirA protein is much less active in these reactions. The biotinylation reaction is proximity-dependent in that a greater extent of biotinylation was seen when the mutant ligase was coupled to the acceptor proteins than when the acceptors were free in solution. This approach may permit facile detection and recovery of interacting proteins by existing avidin/streptavidin technology.     

To age or not to age

According to the antagonistic pleiotropy theory of ageing, natural selection has favoured genes conferring short-term benefits to the organism at the cost of deterioration in later life. The 'disposable soma' theory expresses this as a life-history strategy in which somatic maintenance is below the level required to prevent ageing, thus enabling higher immediate fertility. It has been argued that a non-ageing strategy will always be bettered by a low but non-zero rate of ageing, because the costs of such ageing will be felt only in the distant future when they are of negligible importance. Here, we examine this argument critically. We find that a non-ageing strategy will be locally optimal if, in the presence of ageing, the onset of deterioration is sufficiently rapid or early. Conversely, ageing will be optimal if deterioration is sufficiently slow or late. As the temporal profile of ageing changes from one of steady deterioration to one involving a sudden loss of vitality after a period of little or no decline, the conditions for a non-ageing strategy to be locally optimal become progressively more stringent. But for all forms of profile considered, conditions can be found for which a strategy involving no ageing is locally optimal.     

The evolutionary potential of the Drosophila sex determination gene network

The evolution of sex determination mechanisms is known to be relatively rapid, though recent evidence indicates that certain parts of the mechanism may be more highly conserved. These characteristics establish the sex determination mechanism as a good candidate for the theoretical study of gene network evolution, particularly of networks involved in development. We investigate the short-term evolutionary potential of the sex determination mechanism in Drosophila melanogaster with the aid of a synchronous logical model. We introduce general theoretical concepts such as a network-specific form of mutation, and a notion of functional equivalence between networks. We apply this theoretical framework to the sex determination mechanism and compare it to a population of random networks, enabling us to find features both general to sex determination networks, and particular to the Drosophila network. In general, sex determination networks exist within large sets of functionally equivalent networks all of which satisfy the sex determination task. These large sets are in turn composed of subsets which are mutationally related, suggesting a high degree of flexibility is available without compromising the core functionality. Two particular characteristics of the Drosophila network are found: (a) a parsimonious use of gene interactions, and (b) the network structure can produce a relatively large number of dynamical pattern variations through single network mutations.