The omega equation and potential vorticity

Two fundamental perspectives on the dynamics of midlatitude weather systems are provided by potential vorticity (PV) and the omega equation. The aim of this paper is to investigate the link between the two perspectives, which has so far received very little attention in the meteorological literature. It also aims to give a quantitative basis for discussion of quasi-geostrophic vertical motion in terms of components associated with system movement, maintaining a constant thermal structure, and with the development of that structure. The former links with the isentropic relative-flow analysis technique. Viewed in a moving frame of reference, the measured development of a system depends on the velocity of that frame of reference. The requirement that the development should be a minimum provides a quantitative method for determining the optimum system velocity. The component of vertical velocity associated with development is shown to satisfy an omega equation with forcing determined from the relative advection of interior PV and boundary temperature. The analysis carries through in the presence of diabatic heating provided the omega equation forcing is based on the interior PV and boundary thermal tendencies, including the heating effect. The analysis is shown to be possible also at the level of the semi-geostrophic approximation. The analysis technique is applied to a number of idealized problems that can be considered to be building blocks for midlatitude synoptic-scale dynamics. They focus on the influences of interior PV, boundary temperature, an interior boundary, baroclinic instability associated with two boundaries, and also diabatic heating. In each case, insights yielded by the new perspective are sought into the dynamical behaviour, especially that related to vertical motion. Copyright © 2003 Royal Meteorological Society

Testing the limits of quasi-geostrophic theory: application to observed laboratory flows outside the quasi-geostrophic regime

We compare laboratory observations of equilibrated baroclinic waves in the rotating two-layer annulus, with numerical simulations from a quasi-geostrophic model. The laboratory experiments lie well outside the quasi-geostrophic regime: the Rossby number reaches unity; the depth-to-width aspect ratio is large; and the fluid contains ageostrophic inertia–gravity waves. Despite being formally inapplicable, the quasi-geostrophic model captures the laboratory flows reasonably well. The model displays several systematic biases, which are consequences of its treatment of boundary layers and neglect of interfacial surface tension and which may be explained without invoking the dynamical effects of the moderate Rossby number, large aspect ratio or inertia–gravity waves. We conclude that quasi-geostrophic theory appears to continue to apply well outside its formal bounds.

Omega-3 fatty acids, cardiovascular disease and stability of atherosclerotic plaques

Long-chain n-3 polyunsaturated fatty acids are found in oily fish and in fish oils and similar preparations. Substantial evidence from epidemiological and case-control studies indicates that consumption of fish, oily fish and long-chain n-3 fatty acids reduces risk of cardiovascular mortality. Secondary prevention studies using long-chain n-3 fatty acids in patients post-myocardial infarction have shown a reduction in total and cardiovascular mortality with an especially potent effect on sudden death. Long-chain n-3 fatty acids have been shown to beneficially modify a range of cardiovascular risk factors, which may result in primary cardiovascular prevention. However, reduced non-fatal and fatal events and a reduction in sudden death probably involve other mechanisms. Reduced thrombosis following long-chain n-3 fatty acids may play a role. A decrease in arrhythmias is a favoured mechanism of action of long-chain n-3 fatty acids and is supported by cell culture and animal studies. However human trials using implantable cardiac defibrillators have produced inconsistent findings and a recent meta-analysis does not support this mechanism of action. An alternative mechanism of action may be stabilisation of atherosclerotic plaques by long-chain n-3 fatty acids. This is suggested by one published human study which showed that incorporation of long-chain n-3 fatty acids into plaques collected at carotid endarterectomy resulted in fewer macrophages in the plaque and a morphology indicative of increased stability. These findings are supported from observations in an animal model and suggest that the primary effect of long-chain n-3 fatty acids might be on macrophages within the plaque.

Simulation of crop yields using ERA-40: Limits to skill and nonstationarity in weather-yield relationships

Reanalysis data provide an excellent test bed for impacts prediction systems. because they represent an upper limit on the skill of climate models. Indian groundnut (Arachis hypogaea L.) yields have been simulated using the General Large-Area Model (GLAM) for annual crops and the European Centre for Medium-Range Weather Forecasts (ECMWF) 40-yr reanalysis (ERA-40). The ability of ERA-40 to represent the Indian summer monsoon has been examined. The ability of GLAM. when driven with daily ERA-40 data, to model both observed yields and observed relationships between subseasonal weather and yield has been assessed. Mean yields "were simulated well across much of India. Correlations between observed and modeled yields, where these are significant. are comparable to correlations between observed yields and ERA-40 rainfall. Uncertainties due to the input planting window, crop duration, and weather data have been examined. A reduction in the root-mean-square error of simulated yields was achieved by applying bias correction techniques to the precipitation. The stability of the relationship between weather and yield over time has been examined. Weather-yield correlations vary on decadal time scales. and this has direct implications for the accuracy of yield simulations. Analysis of the skewness of both detrended yields and precipitation suggest that nonclimatic factors are partly responsible for this nonstationarity. Evidence from other studies, including data on cereal and pulse yields, indicates that this result is not particular to groundnut yield. The detection and modeling of nonstationary weather-yield relationships emerges from this study as an important part of the process of understanding and predicting the impacts of climate variability and change on crop yields.

Mutational meltdown in primary endosymbionts: selection limits Muller's ratchet

Background Primary bacterial endosymbionts of insects (p-endosymbionts) are thought to be undergoing the process of Muller's ratchet where they accrue slightly deleterious mutations due to genetic drift in small populations with negligible recombination rates. If this process were to go unchecked over time, theory predicts mutational meltdown and eventual extinction. Although genome degradation is common among p-endosymbionts, we do not observe widespread p-endosymbiont extinction, suggesting that Muller's ratchet may be slowed or even stopped over time. For example, selection may act to slow the effects of Muller's ratchet by removing slightly deleterious mutations before they go to fixation thereby causing a decrease in nucleotide substitutions rates in older p-endosymbiont lineages. Methodology/Principal Findings To determine whether selection is slowing the effects of Muller's ratchet, we determined the age of the Candidatus Riesia/sucking louse assemblage and analyzed the nucleotide substitution rates of several p-endosymbiont lineages that differ in the length of time that they have been associated with their insect hosts. We find that Riesia is the youngest p-endosymbiont known to date, and has been associated with its louse hosts for only 13–25 My. Further, it is the fastest evolving p-endosymbiont with substitution rates of 19–34% per 50 My. When comparing Riesia to other insect p-endosymbionts, we find that nucleotide substitution rates decrease dramatically as the age of endosymbiosis increases. Conclusions/Significance A decrease in nucleotide substitution rates over time suggests that selection may be limiting the effects of Muller's ratchet by removing individuals with the highest mutational loads and decreasing the rate at which new mutations become fixed. This countering effect of selection could slow the overall rate of endosymbiont extinction.

beta-Sheet mediated self-assembly of dipeptides of omega-amino acids and remarkable fibrillation in the solid state

Single crystal X-ray diffraction studies show that the extended structure of dipeptide I Boc-beta-Ala-m-ABA-OMe (m-ABA: meta-aminobenzoic acid) self-assembles in the solid state by intermolecular hydrogen bonding to create an infinite parallel P-sheet structure. In dipeptide II Boc-gamma-Abu-m-ABA-OMe (gamma-Abu: gamma-aminobutyric acid), two such parallel beta-sheets are further cross-linked by intermolecular hydrogen bonding through m-aminobenzoic acid moieties. SEM (scanning electron microscopy) studies reveal that both the peptides I and II form amyloid-like fibrils in the solid state. The fibrils are also found to be stained readily by Congo red, a characteristic feature of the amyloid fiber whose accumulation causes several fatal diseases such as Alzheimer's, prion-protein etc.

Dipeptide nanotubes, with n-terminally located omega-amino acid residues, that are stable proteolytically, thermally, and over a wide range of pH

Two dipeptides containing an N-terminally positioned omega-amino acid residue (beta-alanine/delta-amino valeric acid) self-assembles to form nanotubes in the solid state as well as in aqueous solution. In spite of having hollow nanotubular structures in the solid state and in solution, their self-assembling nature in these two states are different and this leads to the formation of different internal diameters of these nanotubes in solution and in solid state structure. These nanotubes are stable proteolytically, thermally, and over a wide range of pH values (1-13). The role of water molecules in nanotube formation has been investigated in the solid state. These nanotubes can be considered as a new class of dipeptide nanotubes as they are consisting of N-terminally located protease resistant omega-amino acid residues and C-terminally positioned alpha-amino acid residues. These dipeptides can form an interesting class of short peptidic structure that can give rise to stable nanotubular structure upon self-assembly and these nanotubes can be explored in future for potential nanotechnological applications.