Isolation of novel bacteria, including a candidate division, from geothermal soils in New Zealand

We examined bacterial diversity of three geothermal soils in the Taupo Volcanic Zone of New Zealand. Phylogenetic analysis of 16S rRNA genes recovered directly from soils indicated that the bacterial communities differed in composition and richness, and were dominated by previously uncultured species of the phyla Actinobacteria , Acidobacteria , Chloroflexi , Proteobacteria and candidate division OP10. Aerobic, thermophilic, organotrophic bacteria were isolated using cultivation protocols that involved extended incubation times, low-pH media and gellan as a replacement gelling agent to agar. Isolates represented previously uncultured species, genera, classes, and even a new phylum of bacteria. They included members of the commonly cultivated phyla Proteobacteria , Firmicutes , Thermus/Deinococcus , Actinobacteria and Bacteroidetes , as well as more-difficult-to-cultivate groups. Isolates possessing < 85% 16S rRNA gene sequence identity to any cultivated species were obtained from the phyla Acidobacteria , Chloroflexi and the previously uncultured candidate division OP10. Several isolates were prevalent in 16S rRNA gene clone libraries constructed directly from the soils. A key factor facilitating isolation was the use of gellan-solidified plates, where the gellan itself served as an energy source for certain bacteria. The results indicate that geothermal soils are a rich potential source of novel bacteria, and that relatively simple cultivation techniques are practical for isolating bacteria from these habitats.     

Ecology and genetics of hybrid zones in the southern African Pycnonotus bulbul species complex

Lloyd, P., Craig, A.J.F.K., Hulley, P.E., Essop, M.F., Bloomer, P. & Crowe, T.M. 1997. Ecology and genetics of hybrid zones in the southern African Pycnonotus bulbul species complex. Ostrich 68 (2–4): 90–96.

The closely related Blackeyed Bulbul Pycnonotus barbatus, Cape Bulbul P. capensis and Redeyed Bulbul P. nigricans have parapatric to locally sympatric distributions within southern Africa. Extensive hybridization along narrow transition zones between each of the three species pairs is described in a region of the Eastern Cape province, South Africa. The transition zones coincide with ecotones between different vegetation types, which in turn follow escarpments or mountain ranges. The lack of population density depressions within the hybrid zones, together with the variability of the hybrids, suggests the hybrids are viable. Sharp step clines in various phenotypic characters are described across the P. barbatus/P. nigricans hybrid zone. A mtDNA analysis found evidence of possible introgression between P. barbatus and P. capensis. All eight P. barbatus x P. nigricans hybrids analysed possessed P. barbatus mtDNA, suggesting the existence of either positive assortative mating or strong directional selection, but our data are unable to distinguish which. Our results do not support the dynamic-equilibrium model, but are compatible with the bounded-hybrid-superiority model. We conclude that the maintenance of the parapatric distributions of the different taxa is due mainly to differences in environmentally-associated fitness between parental phenotypes or among parental and hybrid phenotypes along an ecotone, with the narrowness of the hybrid zones maintained by the steepness of the environmental gradients crossing them.     

Physical properties of membrane fractions isolated from human platelets: implications for chilling induced platelet activation.

In previous studies, it has been suggested that chilling induced activation of human platelets is related to a lipid phase transition seen in membrane lipids. Those studies showed a single, surprisingly cooperative transition in human platelets, as determined by Fourier transform infrared (FTIR) spectroscopy, findings that are confirmed here with calorimetric measurements. Such transitions have now been studied in membrane fractions obtained from the platelets and it is reported that all fractions and purified phospholipids show similar transitions. In order to obtain these data it was necessary to develop means for separating these fractions. Therefore, a novel method for isolation and separation of dense tubular system (DTS) and plasma membranes in human platelets is described here. Lipid analysis showed that phosphatidylcholine (PC) and phosphatidylethanolamine (PE) were the dominant phospholipids in both fractions, whereas cholesterol and sphingomyelin (SM) were predominantly located in the plasma membranes. Thermotropic phase transitions in the two membrane fractions, determined by differential scanning calorimetry (DSC) and FTIR spectroscopy were found to occur at about 15 degrees C, similar to the Tm of intact human platelets. These data are discussed in relation to the role of the DTS and plasma membranes in the cold-induced activation of human platelets.     

Human Germline Antibody Gene Segments Encode Polyspecific Antibodies

Structural flexibility in germline gene-encoded antibodies allows promiscuous binding to diverse antigens. The binding affinity and specificity for a particular epitope typically increase as antibody genes acquire somatic mutations in antigen-stimulated B cells. In this work, we investigated whether germline gene-encoded antibodies are optimal for polyspecificity by determining the basis for recognition of diverse antigens by antibodies encoded by three V_H gene segments. Panels of somatically mutated antibodies encoded by a common V_H gene, but each binding to a different antigen, were computationally redesigned to predict antibodies that could engage multiple antigens at once. The Rosetta multi-state design process predicted antibody sequences for the entire heavy chain variable region, including framework, CDR1, and CDR2 mutations. The predicted sequences matched the germline gene sequences to a remarkable degree, revealing by computational design the residues that are predicted to enable polyspecificity, i.e., binding of many unrelated antigens with a common sequence. The process thereby reverses antibody maturation in silico. In contrast, when designing antibodies to bind a single antigen, a sequence similar to that of the mature antibody sequence was returned, mimicking natural antibody maturation in silico. We demonstrated that the Rosetta computational design algorithm captures important aspects of antibody/antigen recognition. While the hypervariable region CDR3 often mediates much of the specificity of mature antibodies, we identified key positions in the V_H gene encoding CDR1, CDR2, and the immunoglobulin framework that are critical contributors for polyspecificity in germline antibodies. Computational design of antibodies capable of binding multiple antigens may allow the rational design of antibodies that retain polyspecificity for diverse epitope binding.     

The effects of foliar pubescence and nutrient enrichment on arthropod communities of Metrosideros polymorpha (Myrtaceae)

Abstract.  1. Nutrient resource availability and host-plant foliar pubescence both influence arthropod food webs, but multifactor studies are needed to understand their interdependence and relative importance. Arthropods were sampled by clipping foliage from Metrosideros polymorpha (Myrtaceae) trees of pubescent, glabrous, and intermediate leaf forms on fertilised and unfertilised plots.
2. Fertilisation decreased leaf mass per area (LMA) but did not change the relative mass of pubescence within leaf morphological classes.
3. Fertilisation increased densities of individuals in four taxonomic orders, densities of individuals and species of all trophic levels, and the biomass of Collembola and Homoptera. Herbivore relative diversity (Shannon H ') also increased with fertilisation, but detritivore diversity declined due to increasing dominance of Salina celebensis (Schaeffer) (Collembola).
4. Detritivore density, driven again by S. celebensis , increased with decreasing leaf pubescence, but Heteroptera and Acari were most abundant on the intermediate pubescence class, and Psocoptera density and biomass increased with increasing pubescence. Trophic-level species density did not change with leaf morphological class, but relative diversity of all arthropods and of detritivores increased with increasing pubescence.
5. Both resource availability and leaf pubescence affected Metrosideros arthropod communities. However, the pervasive positive influence of fertilisation did not translate to compositional shifts, and there were no interactions with leaf morphological class. In contrast, the effects of leaf pubescence on arthropod density, biomass, and diversity were more restricted taxonomically, and non-parametric manova and redundancy analyses demonstrated significant differentiation in community composition on the pubescent morphology.     

The spatial dynamics of pollen beetles in relation to inflorescence growth stage of oilseed rape: implications for trap crop strategies

Semi‐field‐scale arrays of oilseed rape (Brassica napus L.) (Brassicaceae) plants were used to observe the development of distributions of pollen beetles (Meligethes aeneus Fabricius) (Coleoptera: Nitidulidae) in a simulated trap crop system where inflorescence growth stage alone was used to manipulate the pest. Over two successive years, pairs of 1 m spaced square arrays of 100 glasshouse‐grown plants were placed 40 m apart in the field in May, and were subject to natural infestation by pollen beetles. The test plot of each pair had a simulated trap crop, with an outer row of plants at early flowering stage intended to protect more susceptible inner plants at late bud stage, and the control plot had all plants at the late‐bud stage, simulating a standard crop situation. Pollen beetles were counted daily on each plant for 10–13 days. The spatio‐temporal development of plot infestation was analysed in relation to the distribution of racemes in bud and raceme in flowers using Spatial Analysis by Distance IndicEs (SADIE), and tests of edge and centre distribution. Inflorescence growth stage characteristics were shown to be important in determining the spatial distributions of pollen beetles. In control plots, the numbers of racemes in bud and in flower were never edge or centre distributed. In test plots, racemes in flower were always edge distributed, and racemes in bud began edge distributed and became centre distributed. Pollen beetle numbers were usually spatially associated with the abundance of racemes in bud and/or in flower. In control plots, pollen beetles were neither edge nor centre distributed, but in test plots they maintained a significant edge distribution for 7–10 days. At the end of the experiments, females were more centre distributed in the test plots than males, and were more closely associated with racemes with buds, whereas males were more associated with racemes with flowers. In early flowering stage plants, the number of racemes in flowers were a good indicator of the abundance of racemes in buds, but this relationship was lost as flowering progressed. Although flowering racemes provide strong cues for immigrating pollen beetles, the abundance of buds may be a more important determinant of residence time, particularly for females, and is therefore a critical determinant of trap crop effectiveness.     

Relative performance of Lindgren multiple-funnel, Intercept panel, and Colossus pipe traps in catching Cerambycidae and associated species in the southeastern United States

In 2004, we evaluated the relative performance of 8-unit Lindgren multiple-funnel (funnel), Intercept panel (panel), and Colossus pipe (pipe) traps, baited with ethanol and ac-pinene lures, in catching saproxylic beetles (Coleoptera) in pine stands in northern Florida and western South Carolina. Panel traps were as good as, if not better than, funnel and pipe traps for catching Cerambycidae. In particular, more Monochamus titillator (F.) were captured in panel traps than in pipe and funnel traps. Of three species of Buprestidae captured in our study, most Buprestis lineata F. were caught in panel traps, whereas most Acmaeodera tubulus (F.) were caught in funnel traps. Catches of Chalcophora virginiensis Drury and the root-feeding weevils Hylobius pales Herbst an dPachylobius picivorus LeConte (Curculionidae) were unaffected by trap type. Among bark beetles (Curculionidae: Scolytinae), catches of Ips grandicollis (Eichhoff) were unaffected by trap type, whereas most Dendroctonus terebrans (Olivier) were caught in panel traps, most Hylastes salebrosus Eichhoff were caught in panel and pipe traps, and most Hylastes tenuis Eichhoff were caught in funnel traps. Among ambrosia beetles (Curculionidae: Scolytinae), panel traps caught the most Xyleborinus saxesenii (Ratzeburg), whereas pipe traps caught the most Xyleborus Eichhoff spp. More Xylosandrus crassiusculus (Motschulsky) and Dryoxylon onoharaensis (Murayama) were caught in panel and funnel traps than in pipe traps. Among bark beetle predators, more Platysoma Leach spp. (Histeridae) were caught in pipe and panel traps than in funnel traps, whereas most Lasconotus Erichson spp. (Zopheridae) were caught in funnel traps. Variation among trap performance for various species suggests that managers should consider more than one type of trap in their detection programs.     

Heteroalicyclic carboxamidines as inhibitors of inducible nitric oxide synthase; the identification of (2R)-2-pyrrolidinecarboxamidine as a potent and selective haem-co-ordinating inhibitor

Heteroalicyclic carboxamidines were synthesised and evaluated as inhibitors of nitric oxide synthases. (2R)-2-Pyrrolidinecarboxamidine, in particular, was shown to be a highly potent in vitro (IC₅₀ = 0.12 μM) and selective iNOS inhibitor (>100-fold vs both eNOS and nNOS), with probable binding to the key anchoring glutamate residue and co-ordination to the haem iron.     

Genetic structure of the stonefly, Yoraperla brevis, populations: the extent of gene flow among adjacent montane streams

1. Gene flow in populations of stream insects is expected to depend on the distance between and the connectedness of sites in stream networks, and on dispersal ability (i.e. larval drift and adult flight).
2. Yoraperla brevis (Banks) is an abundant and characteristic stonefly of smaller streams in the northern Rocky Mountains. The present authors analysed genetic structure at 27 sites in sevenz streams flowing into the Bitterroot River in western Montana, USA. Cellulose acetate electrophoresis identified five variable loci with 16 alleles.
3. Genotype frequencies conformed to Hardy–Weinberg expectations. Within-stream differentiation was low and among-stream variation ( F _st) was an order of magnitude higher.
4. UPGMA grouped sites within streams and also grouped adjacent streams. The tree produced by the Neighbour Joining Method was similar although not quite so clear cut.
5. This orderly pattern (i.e. Hardy–Weinberg proportions, homogeneity within streams and geographical structure) contrasts strongly with patterns observed in invertebrates from subtropical streams in Australia. Yoraperla brevis maintains large populations in predictable environments, has a long life-cycle with a likelihood of cohort mixing, emerges synchronously in large breeding populations and occupies streams separated by areas of high relief; the Australian situation is the opposite in most respects.
6. Further analysis of a range of species is required to determine whether the different genetic structure in Y. brevis compared to the Australian species occurs more generally in North American stream insects.