Inertia-Gravity Waves Emitted from Balanced Flow: Observations, Properties, and Consequences

This paper describes laboratory observations of inertia–gravity waves emitted from balanced fluid flow. In a rotating two-layer annulus experiment, the wavelength of the inertia–gravity waves is very close to the deformation radius. Their amplitude varies linearly with Rossby number in the range 0.05–0.14, at constant Burger number (or rotational Froude number). This linear scaling challenges the notion, suggested by several dynamical theories, that inertia–gravity waves generated by balanced motion will be exponentially small. It is estimated that the balanced flow leaks roughly 1% of its energy each rotation period into the inertia–gravity waves at the peak of their generation. The findings of this study imply an inevitable emission of inertia–gravity waves at Rossby numbers similar to those of the large-scale atmospheric and oceanic flow. Extrapolation of the results suggests that inertia–gravity waves might make a significant contribution to the energy budgets of the atmosphere and ocean. In particular, emission of inertia–gravity waves from mesoscale eddies may be an important source of energy for deep interior mixing in the ocean.

A hierarchical Bayesian model for predicting the functional consequences of amino-acid polymorphisms

Genetic polymorphisms in deoxyribonucleic acid coding regions may have a phenotypic effect on the carrier, e.g. by influencing susceptibility to disease. Detection of deleterious mutations via association studies is hampered by the large number of candidate sites; therefore methods are needed to narrow down the search to the most promising sites. For this, a possible approach is to use structural and sequence-based information of the encoded protein to predict whether a mutation at a particular site is likely to disrupt the functionality of the protein itself. We propose a hierarchical Bayesian multivariate adaptive regression spline (BMARS) model for supervised learning in this context and assess its predictive performance by using data from mutagenesis experiments on lac repressor and lysozyme proteins. In these experiments, about 12 amino-acid substitutions were performed at each native amino-acid position and the effect on protein functionality was assessed. The training data thus consist of repeated observations at each position, which the hierarchical framework is needed to account for. The model is trained on the lac repressor data and tested on the lysozyme mutations and vice versa. In particular, we show that the hierarchical BMARS model, by allowing for the clustered nature of the data, yields lower out-of-sample misclassification rates compared with both a BMARS and a frequen-tist MARS model, a support vector machine classifier and an optimally pruned classification tree.

The population dynamical consequences of density-dependence in fungal plant pathogens

Almost all stages of a plant pathogen life cycle are potentially density dependent. At small scales and short time spans appropriate to a single-pathogen individual, density dependence can be extremely strong, mediated both by simple resource use, changes in the host due to defence reactions and signals between fungal individuals. In most cases, the consequences are a rise in reproductive rate as the pathogen becomes rarer, and consequently stabilisation of the population dynamics; however, at very low density reproduction may become inefficient, either because it is co-operative or because heterothallic fungi do not form sexual spores. The consequence will be historically determined distributions. On a medium scale, appropriate for example to several generations of a host plant, the factors already mentioned remain important but specialist natural enemies may also start to affect the dynamics detectably. This could in theory lead to complex (e.g. chaotic) dynamics, but in practice heterogeneity of habitat and host is likely to smooth the extreme relationships and make for more stable, though still very variable, dynamics. On longer temporal and longer spatial scales evolutionary responses by both host and pathogen are likely to become important, producing patterns which ultimately depend on the strength of interactions at smaller scales.

Modification of hemicellulose content by antisense down-regulation of UDP-glucuronate decarboxylase in tobacco and its consequences for cellulose extractability

Extractability and recovery of cellulose from cell walls influences many industrial processes and also the utilisation of biomass for energy purposes. The utility of genetic manipulation of lignin has proven potential for optimising such processes and is also advantageous for the environment. Hemicelluloses, particularly secondary wall xylans, also influence the extractability of cellulose. UDP-glucuronate decarboxylase produces UDP-xylose, the precursor for xylans and the effect of its down-regulation on cell wall structure and cellulose extractability in transgenic tobacco has been investigated. Since there are a number of potential UDP-glucuronate decarboxylase genes, a 490 bp sequence of high similarity between members of the family, was chosen for general alteration of the expression of the gene family. Sense and antisense transgenic lines were analysed for enzyme activity using a modified and optimised electrophoretic assay, for enzyme levels by western blotting and for secondary cell wall composition. Some of the down-regulated antisense plants showed high glucose to xylose ratios in xylem walls due to less xylose-containing polymers, while arabinose and uronic acid contents, which could also have been affected by any change in UDP-xylose provision, were unchanged. The overall morphology and stem lignin content of the modified lines remained little changed compared with wild-type. However, there were some changes in vascular organisation and reduction of xylans in the secondary walls was confirmed by immunocytochemistry. Pulping analysis showed a decreased pulp yield and a higher Kappa number in some lines compared with controls, indicating that they were less delignified, although the level of residual alkali was reduced. Such traits probably indicate that lignin was less available for removal in a reduced background of xylans. However, the viscosity was higher in most antisense lines, meaning that the cellulose was less broken-down during the pulping process. This is one of the first studies of a directed manipulation of hemicellulose content on cellulose extractability and shows both positive and negative outcomes.

The costs and consequences of parasitoid attack for the predatory hoverfly, Episyrphus balteatus

Question: What are the life-history costs for a predatory insect of surviving parasitoid attack, and can parasitoid attack alter predator-prey interactions? Hypotheses: Survivorship is influenced by host age. Hosts that suffer parasitoid attack grow more slowly and consume fewer prey. Those that survive attack are smaller as adults and show reduced survivorship. Organisms: The aphidophagous hoverfly Episyrphus balteatus, its endoparasitoid wasp Diplazon laetatorius and its prey, the pea aphid, Acyrthosiphon pisum. Site of experiments: All experiments were conducted in controlled temperature rooms and chambers in the laboratory. Methods: Episyrphus balteatus larvae of each instar were exposed to attack by Diplazon laetatorius, then dissected to measure the encapsulation response (a measure of immunity). Second instar larvae were either attacked or not attacked by D. laetatorius. Their development rates and numbers of prey consumed were noted. The size and survivorship of surviving (immune) and control hoverflies were compared following eclosion. Conclusions: Successful immune response increased with larval age (first instar 0%, second instar 40%, third instar 100% survival). Second instar larvae that successfully resisted parasitoid attack were larger as pupae (but not as adults) and showed reduced adult survivorship. Female adult survivors were more likely than male survivors to have died within 16 days of eclosion, but there was no difference between unattacked male and female control hoverflies. Attacked larvae, irrespective of immune status, consumed fewer aphids than unattacked individuals. Episyrphus balteatus suffers significant costs of resisting parasitoid attack, and parasitoid attack can reduce the top-down effects of an insect predator, irrespective of whether the host mounts an immune response or not.

Multiple domestications and their taxonomic consequences: the example of Phaseolus vulgaris

The evolutionary history of P. vulgaris is important to those working on its genetic resources, but is not reflected in its infraspecific taxonomy. Genetic isolation of wild populations between and also within Middle and South America has resulted in morphological and molecular differentiation. Populations from northern and southern ends of the range are assigned to different gene pools, though intermediates occur in intervening areas. Chloroplast haplotypes suggest three distinct lineages of wild beans and several intercontinental dispersals. The species was domesticated independently in both Middle and South America, probably several times in Middle America. This, together with further differentiation under human selection, has produced distinct races among domesticated beans. The informal categories of wild versus domesticated, gene pool, and race convey the evolutionary picture more clearly than the formal categories provided by the Codes of Nomenclature for wild or cultivated plants.

Consequences of N,C,N '- and C,N,N '-coordination modes on electronic and photophysical properties of cyclometalated aryl ruthenium(II) complexes

The effects of isoelectronic replacement of a neutral nitrogen donor atom by an anionic carbon atom in terpyridine ruthenium(II) complexes on the electronic and photophysical properties of the resulting N,C,N'- and C,N,N'-cyclometalated aryl ruthenium(II) complexes were investigated. To this end, a series of complexes was prepared either with ligands containing exclusively nitrogen donor atoms, that is, [Ru(R-1-tpy)(R-2-tpy)](2+) (R-1, R-2 = H, CO2Et), or bearing either one N,C,N'- or C,N,N'-cyclometalated ligand and one tpy ligand, that is, [Ru(R-1-(NCN)-C-Lambda-N-Lambda)(R-2-tpy)](+) and [Ru(R-1-(CNN)-N-Lambda-N-Lambda)(R-2-tpy)](+), respectively. Single-crystal X-ray structure determinations showed that cyclometalation does not significantly alter the overall geometry of the complexes but does change the bond lengths around the ruthenium(II) center, especially the nitrogen-to-ruthenium bond length trans to the carbanion. Substitution of either of the ligands with electron-withdrawing ester functionalities fine-tuned the electronic properties and resulted in the presence of an IR probe. Using trends obtained from redox potentials, emission energies, IR spectroelectrochemical responses, and the character of the lowest unoccupied molecular orbitals from DFT studies, it is shown that the first reduction process and luminescence are associated with the ester-substituted C,N,N'-cyclometalated ligand in [Ru(EtO2C-(CNN)-N-Lambda-N-Lambda)(tpy)](+). Cyclometalation in an N,C,N'-bonding motif changed the energetic order of the ruthenium d(zx), d(yz), and d(xy) orbitals. The red-shifted absorption in the N,C,N'-cyclometalated complexes is assigned to MLCT transitions to the tpy ligand. The red shift observed upon introduction of the ester moiety is associated with an increase in intensity of low-energy transitions, rather than a red shift of the main transition. Cyclometalation in the C,N,N'-binding motif also red-shifts the absorption, but the corresponding transition is associated with both ligand types. Luminescence of the cyclometalated complexes is relatively independent of the mode of cyclometalation, obeying the energy gap law within each individual series.

Using what we know: consequences of intentionally retrieving gist versus item-specific information

The effect of a prior gist-based versus item-specific retrieval orientation on recognition of objects and words was examined. Prior item-specific retrieval increased item-specific recognition of episodically related but not previously tested objects relative to both conceptual- and perceptual-gist retrieval. An item-specific retrieval advantage also was found when the stimuli were words (synonyms) rather than objects but not when participants overtly named objects during gist-based recognition testing, which suggests that they did not always label objects under general gist-retrieval instructions. Unlike verbal overshadowing, labeling objects during recognition attenuated (but did not eliminate) test- and interference-related forgetting. A full understanding of how retrieval affects subsequent memory, even for events or facts that are not themselves retrieved, must take into account the specificity with which that retrieval occurs.