Arthrobacter nasiphocae sp. nov., from the common seal (Phoca vitulina)

An unknown gram-positive, catalase-positive, strictly aerobic, rod-shaped bacterium was isolated from the nasal cavities of two common seals. Chemical analysis revealed the presence in the bacterium of a hitherto unknown cell-wall murein [type: L-Lys-L-Ala2-Gly(2-3)-L-Ala (Gly)]. Comparative 16S rRNA gene sequencing showed that the unidentified rod was related to the Arthrobacter group of organisms, although sequence divergence values of >3% from established members of this genus indicated that it represents a novel species. On the basis of phenotypic and phylogenetic considerations, it is proposed that the unknown bacterium from seals (Phoca vitulina) be classified as a novel species, Arthrobacter nasiphocae sp. nov. The type strain of Arthrobacter nasiphocae is CCUG 42953T.

Corynebacterium testudinoris sp. nov., from a tortoise, and Corynebacterium felinum sp. nov., from a Scottish wild cat

Two unknown gram-positive, rod-shaped bacteria isolated from a tortoise and a Scottish wild cat were subjected to a polyphasic taxonomic analysis. Chemical analysis revealed the presence of straight-chain and monounsaturated fatty acids and short-chain mycolic acids in the two isolates consistent with the genus Corynebacterium. Comparative 16S rRNA gene sequencing confirmed that the unknown isolates were members of the genus Corynebacterium, with the two organisms displaying greater than 3% sequence divergence from each other and from established species of the genus. The unknown Corynebacterium isolates were readily distinguished from each other and from all recognized species of the genus by biochemical tests. Based on phylogenetic and phenotypic evidence, it is proposed that the unknown organisms from a tortoise and a cat be classified in the genus Corynebacterium as Corynebacterium testudinoris sp. nov. and Corynebacterium felinum sp. nov., respectively. The respective type strains of C. testudinoris and C. felinum are CCUG 41823T and CCUG 39943T.

Corynebacterium capitovis sp. nov., from a sheep

An unknown Gram-positive rod-shaped bacterium was isolated from skin scrapings from the infected head of a sheep and subjected to a polyphasic taxonomic analysis. Chemical analysis revealed the presence of straight-chain and monounsaturated fatty acids and short-chain (C32-C36) mycolic acids consistent with the genus Corynebacterium. Comparative 16S rRNA gene sequencing confirmed that the unknown rod was a member of the genus Corynebacterium, with the organism forming a distinct sub-line and displaying greater than 3% sequence divergence with established species. The unknown Corynebacterium isolate was readily distinguished from recognized species of the genus by biochemical tests and electrophoretic analysis of whole-cell proteins. Based on phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium from a sheep be classified in the genus Corynebacterium, as Corynebacterium capitovis sp. nov. The type strain of Corynebacterium capitovis is CCUG 39779T (= CIP 106739T).

Actinomyces marimammalium sp. nov., from marine mammals

Three strains of a previously undescribed Actinomyces-like bacterium were isolated from samples taken from two dead seals and a porpoise. Biochemical testing and PAGE analysis of whole-cell proteins indicated the strains were phenotypically similar to each other but different from previously described Actinomyces and Arcanobacterium species. Comparative 16S rRNA gene sequencing studies showed the organisms from marine animals were genetically closely related and represent a hitherto unknown subline within the genus Actinomyces (sequence divergence values > 6% with recognized species). Based on phylogenetic and phenotypic evidence it is proposed that the unknown bacterium from the seals and a porpoise should be classified as Actinomyces marimammalium sp. nov. The type strain is CCUG 41710T.

Actinomyces canis sp. nov., isolated from dogs

Three strains of a previously undescribed catalase-positive Actinomyces-like bacterium were isolated from dogs. Biochemical testing and PAGE analysis of whole-cell proteins indicated that the strains were phenotypically highly related to each other but different from previously described Actinomyces and Arcanobacterium species. Sequencing of 16S rRNA showed that the unknown bacterium represents a new subline within a cluster of species which includes Actinomyces hyovaginalis, Actinomyces georgiae, Actinomyces meyeri, Actinomyces odontolyticus, Actinomyces radingae and Actinomyces turicensis. On the basis of phenotypic evidence and 16S rRNA sequence divergence levels (greater than 5% with recognized Actinomyces species) it is proposed that the unknown strains from canine sources be classified as a new species with the name Actinomyces canis sp. nov. The type strain of Actinomyces canis is CCUG 41706T (= CIP 106351T).

Differential recognition of Staphylococcus aureus quorum-sensing signals depends on both extracellular loops 1 and 2 of the transmembrane sensor AgrC.

Virulence in Staphylococcus aureus is regulated via agr-dependent quorum sensing in which an autoinducing peptide (AIP) activates AgrC, a histidine protein kinase. AIPs are usually thiolactones containing seven to nine amino acid residues in which the thiol of the central cysteine is linked to the alpha-carboxyl of the C-terminal amino acid residue. The staphylococcal agr locus has diverged such that the AIPs of the four different S. aureus agr groups self-activate but cross-inhibit. Consequently, although the agr system is conserved among the staphylococci, it has undergone significant evolutionary divergence whereby to retain functionality, any changes in the AIP-encoding gene (agrD) that modifies AIP structure must be accompanied by corresponding changes in the AgrC receptor. Since AIP-1 and AIP-4 only differ by a single amino acid, we compared the transmembrane topology of AgrC1 and AgrC4 to identify amino acid residues involved in AIP recognition. As only two of the three predicted extracellular loops exhibited amino acid differences, site-specific mutagenesis was used to exchange the key AgrC1 and AgrC4 amino acid residues in each loop either singly or in combination. A novel lux-based agrP3 reporter gene fusion was constructed to evaluate the response of the mutated AgrC receptors. The data obtained revealed that while differential recognition of AIP-1 and AIP-4 depends primarily on three amino acid residues in loop 2, loop 1 is essential for receptor activation by the cognate AIP. Furthermore, a single mutation in the AgrC1 loop 2 resulted in conversion of (Ala5)AIP-1 from a potent antagonist to an activator, essentially resulting in the forced evolution of a new AIP group. Taken together, our data indicate that loop 2 constitutes the predicted hydrophobic pocket that binds the AIP thiolactone ring while the exocyclic amino acid tail interacts with loop 1 to facilitate receptor activation.

Speciation as an active force in promoting genetic evolution

There is a growing appreciation among evolutionary biologists that the rate and tempo of molecular evolution might often be altered at or near the time of speciation, i.e. that speciation is in some way a special time for genes. Molecular phylogenies frequently reveal increased rates of genetic evolution associated with speciation and other lines of investigation suggest that various types of abrupt genomic disruption can play an important role in promoting speciation via reproductive isolation. These phenomena are in conflict with the gradual view of molecular evolution that is implicit in much of our thinking about speciation and in the tools of modern biology. This raises the prospect of studying the molecular evolutionary consequences of speciation per se and studying the footprint of speciation as an active force in promoting genetic divergence. Here we discuss the reasons to believe that speciation can play such a role and elaborate on possible mechanisms for accelerated rates of evolution following speciation. We provide an example of how it is possible detect whether accelerated bursts of evolution occur in neutral and/or adaptive regions of genes and discuss the implications of rapid episodes of change for conventional models of molecular evolution. Speciation might often owe more to ephemeral and essentially arbitrary events that cause reproductive isolation than to the gradual and regular tug of natural selection that draws a species into a new niche.

Progressive erosion of genetic and epigenetic variation in callus-derived cocoa (Theobroma cacao) plants

Relatively little is known about the timing of genetic and epigenetic forms of somaclonal variation arising from callus growth. We surveyed for both types of change in cocoa (Theobroma cacao) plants regenerated from calli of various ages, and also between tissues from the source trees. For genetic change, we used 15 single sequence repeat (SSR) markers from four source trees and from 233 regenerated plants. For epigenetic change, we used 386 methylation-sensitive amplified polymorphism (MSAP) markers on leaf and explant (staminode) DNA from two source trees and on leaf DNA from 114 regenerants. Genetic variation within source trees was limited to one slippage mutation in one leaf. Regenerants were far more variable, with 35% exhibiting at least one mutation. Genetic variation initially accumulated with culture age but subsequently declined. MSAP (epigenetic) profiles diverged between leaf and staminode samples from source trees. Multivariate analysis revealed that leaves from regenerants occupied intermediate eigenspace between leaves and staminodes of source plants but became progressively more similar to source tree leaves with culture age. Statistical analysis confirmed this rather counterintuitive finding that leaves of ‘late regenerants’ exhibited significantly less genetic and epigenetic divergence from source leaves than those exposed to short periods of callus growth.

Impact of age and menopausal status on the postprandial triacylglycerol response in healthy women

Objective: To examine the impact of age and the natural menopause on the postprandial triacylglycerol (TAG) response in healthy women. Methods and results: Thirty-seven premenopausal and sixty-one postmenopausal women underwent a sequential meal postprandial investigation, in which blood samples were taken at regular intervals after a test breakfast and lunch given at 0 and 330 min respectively. Lipids and glucose were measured in the fasting sample, with TAG analysed in the postprandial samples. Postmenopausal women were shown to have higher fasting total cholesterol, low density lipoprotein cholesterol (LDL-C) and glucose (P < 0.02). Marked differences in the postprandial TAG response were evident between the groups, with a greater incremental area under the curve (IAUC) and maximum TAG concentration in the postmenopausal women (P < 0.04). Multivariate regression analysis revealed both age and fasting TAG to be independently associated with the summary measures of the postprandial TAG response in the premenopausal women only. Interestingly, sub-division of the women into both younger and older pre- and postmenopausal subgroups, showed the most marked difference in TAG-IAUC to be between the younger and the older premenopausal women, whereas differences in fasting LDL-C were most evident between the older premenopausal and the younger postmenopausal women. Conclusions: Our results suggest a divergence in the relationship of age and menopausal status with fasting LDL-C and postprandial TAG which may reflect differences in the metabolic effects of age and the menopause on these lipid risk markers or a greater impact of early oestrogen decline on pathways of TAG rather than LDL metabolism.

Ensemble prediction for nowcasting with a convection-permitting model - II: forecast error statistics

A 24-member ensemble of 1-h high-resolution forecasts over the Southern United Kingdom is used to study short-range forecast error statistics. The initial conditions are found from perturbations from an ensemble transform Kalman filter. Forecasts from this system are assumed to lie within the bounds of forecast error of an operational forecast system. Although noisy, this system is capable of producing physically reasonable statistics which are analysed and compared to statistics implied from a variational assimilation system. The variances for temperature errors for instance show structures that reflect convective activity. Some variables, notably potential temperature and specific humidity perturbations, have autocorrelation functions that deviate from 3-D isotropy at the convective-scale (horizontal scales less than 10 km). Other variables, notably the velocity potential for horizontal divergence perturbations, maintain 3-D isotropy at all scales. Geostrophic and hydrostatic balances are studied by examining correlations between terms in the divergence and vertical momentum equations respectively. Both balances are found to decay as the horizontal scale decreases. It is estimated that geostrophic balance becomes less important at scales smaller than 75 km, and hydrostatic balance becomes less important at scales smaller than 35 km, although more work is required to validate these findings. The implications of these results for high-resolution data assimilation are discussed.

Patterns of nucleotide substitution in angiosperm cpDNA trnL (UAA)-trnF (GAA) regions

Patterns of substitution in chloroplast encoded trnL_F regions were compared between species of Actaea (Ranunculales), Digitalis (Scrophulariales), Drosera (Caryophyllales), Panicoideae (Poales), the small chromosome species clade of Pelargonium (Geraniales), each representing a different order of flowering plants, and Huperzia (Lycopodiales). In total, the study included 265 taxa, each with > 900-bp sequences, totaling 0.24 Mb. Both pairwise and phylogeny-based comparisons were used to assess nucleotide substitution patterns. In all six groups, we found that transition/transversion ratios, as estimated by maximum likelihood on most-parsimonious trees, ranged between 0.8 and 1.0 for ingroups. These values occurred both at low sequence divergences, where substitutional saturation, i.e., multiple substitutions having occurred at the same (homologous) nucleotide position, was not expected, and at higher levels of divergence. This suggests that the angiosperm trnL-F regions evolve in a pattern different from that generally observed for nuclear and animal mtDNA (transitional/transversion ratio > or = 2). Transition/transversion ratios in the intron and the spacer region differed in all alignments compared, yet base compositions between the regions were highly similar in all six groups. A>-C transversions were significantly less frequent than the other four substitution types. This correlates with results from studies on fidelity mechanisms in DNA replication that predict A<->T and G<->C transversions to be least likely to occur. It therefore strengthens confidence in the link between mutation bias at the polymerase level and the actual fixation of substitutions as recorded on evolutionary trees, and concomitantly, in the neutrality of nucleotide substitutions as phylogenetic markers.

Comparisons of host mitochondrial, nuclear and endosymbiont bacterial genes reveal cryptic fig wasp species and the effects of Wolbachia on host mtDNA evolution and diversity

Background Figs and fig-pollinating wasp species usually display a highly specific one-to-one association. However, more and more studies have revealed that the "one-to-one" rule has been broken. Co-pollinators have been reported, but we do not yet know how they evolve. They may evolve from insect speciation induced or facilitated by Wolbachia which can manipulate host reproduction and induce reproductive isolation. In addition, Wolbachia can affect host mitochondrial DNA evolution, because of the linkage between Wolbachia and associated mitochondrial haplotypes, and thus confound host phylogeny based on mtDNA. Previous research has shown that fig wasps have the highest incidence of Wolbachia infection in all insect taxa, and Wolbachia may have great influence on fig wasp biology. Therefore, we look forward to understanding the influence of Wolbachia on mitochondrial DNA evolution and speciation in fig wasps. Results We surveyed 76 pollinator wasp specimens from nine Ficus microcarpa trees each growing at a different location in Hainan and Fujian Provinces, China. We found that all wasps were morphologically identified as Eupristina verticillata, but diverged into three clades with 4.22-5.28% mtDNA divergence and 2.29-20.72% nuclear gene divergence. We also found very strong concordance between E. verticillata clades and Wolbachia infection status, and the predicted effects of Wolbachia on both mtDNA diversity and evolution by decreasing mitochondrial haplotypes. Conclusions Our study reveals that the pollinating wasp E. verticillata on F. microcarpa has diverged into three cryptic species, and Wolbachia may have a role in this divergence. The results also indicate that Wolbachia strains infecting E. verticillata have likely resulted in selective sweeps on host mitochondrial DNA.

Rational speculative bubbles: an empirical investigation of the London Stock Exchange

In recent years, a sharp divergence of London Stock Exchange equity prices from dividends has been noted. In this paper, we examine whether this divergence can be explained by reference to the existence of a speculative bubble. Three different empirical methodologies are used: variance bounds tests, bubble specification tests, and cointegration tests based on both ex post and ex ante data. We find that, stock prices diverged significantly from their fundamental values during the late 1990's, and that this divergence has all the characteristics of a bubble.

Monetary integration and real estate markets: an investigation of the impact of the introduction of a single currency on real estate performance

This paper assesses the impact of the monetary integration on different types of stock returns in Europe. In order to isolate European factors, the impact of global equity integration and small cap factors are investigated. European countries are sub-divided according to the process of monetary convergence. Analysis shows that national equity indices are strongly influenced by global market movements, with a European stock factor providing additional explanatory power. The global and European factors explain small cap and real estate stocks much less well –suggesting an increased importance of ‘local’ drivers. For real estate, there are notable differences between core and non-core countries. Core European countries exhibit convergence – a convergence to a European rather than a global factor. The non-core countries do not seem to exhibit common trends or movements. For the non-core countries, monetary integration has been associated with increased dispersion of returns, lower correlation and lower explanatory power of a European factor. It is concluded that this may be explained by divergence in underlying macro-economic drivers between core and non-core countries in the post-Euro period.

Amphioxus type I keratin cDNA and the evolution of intermediate filament genes

We report the cloning of an intermediate filament (IF) cDNA from the cephalochordate amphioxus that encodes a protein assignable to the type I keratin group. This is the first type I keratin reported from an invertebrate. Molecular phylogenetic analyses reveal that amphioxus also possesses a type II keratin, and that the genes encoding short-rod IF proteins underwent different patterns of duplication in vertebrates and their closest relatives, the cephalochordates. Extensive IF gene duplication and divergence may have facilitated the origin of new specialised cell types in vertebrates.