The influence of bottom topography on the decay of modeled Agulhas rings

The influence of a large meridional submarine ridge on the decay of Agulhas rings is investigated with a 1 and 2-layer setup of the isopycnic primitive-equation ocean model MICOM. In the single-layer case we show that the SSH decay of the ring is primarily governed by bottom friction and secondly by the radiation of Rossby waves. When a topographic ridge is present, the effect of the ridge on SSH decay and loss of tracer from the ring is negligible. However, the barotropic ring cannot pass the ridge due to energy and vorticity constraints. In the case of a two-layer ring the initial SSH decay is governed by a mixed barotropic–baroclinic instability of the ring. Again, radiation of barotropic Rossby waves is present. When the ring passes the topographic ridge, it shows a small but significant stagnation of SSH decay, agreeing with satellite altimetry observations. This is found to be due to a reduction of the growth rate of the m = 2 instability, to conversions of kinetic energy to the upper layer, and to a decrease in Rossby-wave radiation. The energy transfer is related to the fact that coherent structures in the lower layer cannot pass the steep ridge due to energy constraints. Furthermore, the loss of tracer from the ring through filamentation is less than for a ring moving over a flat bottom, related to a decrease in propagation speed of the ring. We conclude that ridges like the Walvis Ridge tend to stabilize a multi-layer ring and reduce its decay.

Aberrant mRNA Transcripts and the Nonsense-Mediated Decay Proteins UPF2 and UPF3 Are Enriched in the Arabidopsis Nucleolus

The eukaryotic nucleolus is multifunctional and involved in the metabolism and assembly of many different RNAs and ribonucleoprotein particles as well as in cellular functions, such as cell division and transcriptional silencing in plants. We previously showed that Arabidopsis thaliana exon junction complex proteins associate with the nucleolus, suggesting a role for the nucleolus in mRNA production. Here, we report that the plant nucleolus contains mRNAs, including fully spliced, aberrantly spliced, and single exon gene transcripts. Aberrant mRNAs are much more abundant in nucleolar fractions, while fully spliced products are more abundant in nucleoplasmic fractions. The majority of the aberrant transcripts contain premature termination codons and have characteristics of nonsense-mediated decay (NMD) substrates. A direct link between NMD and the nucleolus is shown by increased levels of the same aberrant transcripts in both the nucleolus and in Up-frameshift (upf) mutants impaired in NMD. In addition, the NMD factors UPF3 and UPF2 localize to the nucleolus, suggesting that the Arabidopsis nucleolus is therefore involved in identifying aberrant mRNAs and NMD.

On the fast decay of Agulhas rings

The Indian Ocean water that ends up in the Atlantic Ocean detaches from the Agulhas Current retroflection predominantly in the form of Agulhas rings and cyclones. Using numerical Lagrangian float trajectories in a high-resolution numerical ocean model, the fate of coherent structures near the Agulhas Current retroflection is investigated. It is shown that within the Agulhas Current, upstream of the retroflection, the spatial distributions of floats ending in the Atlantic Ocean and floats ending in the Indian Ocean are to a large extent similar. This indicates that Agulhas leakage occurs mostly through the detachment of Agulhas rings. After the floats detach from the Agulhas Current, the ambient water quickly looses its relative vorticity. The Agulhas rings thus seem to decay and loose much of their water in the Cape Basin. A cluster analysis reveals that most water in the Agulhas Current is within clusters of 180 km in diameter. Halfway in the Cape Basin there is an increase in the number of larger clusters with low relative vorticity, which carry the bulk of the Agulhas leakage transport through the Cape Basin. This upward cascade with respect to the length scales of the leakage, in combination with a power law decay of the magnitude of relative vorticity, might be an indication that the decay of Agulhas rings is somewhat comparable to the decay of two-dimensional turbulence.

Interactions of decay-accelerating factor (DAF) with haemagglutinating human enteroviruses: utilizing variation in primate DAF to map virus binding sites

A cellular receptor for the haemagglutinating enteroviruses (HEV), and the protein that mediates haemagglutination, is the membrane complement regulatory protein decay accelerating factor (DAF; CD55). Although primate DAF is highly conserved, significant differences exist to enable cell lines derived from primates to be utilized for the characterization of the DAF binding phenotype of human enteroviruses. Thus, several distinct DAF-binding phenotypes of a selection of HEVs (viz. coxsackievirus A21 and echoviruses 6, 7, 11-13, 29) were identified from binding and infection assays using a panel of primate cells derived from human, orang-utan, African Green monkey and baboon tissues. These studies complement our recent determination of the crystal structure of SCR(34) of human DAF [Williams, P., Chaudhry, Y., Goodfellow, I. G., Billington, J., Powell, R., Spiller, O. B., Evans, D. J. & Lea, S. (2003). J Biol Chem 278, 10691-10696] and have enabled us to better map the regions of DAF with which enteroviruses interact and, in certain cases, predict specific virus-receptor contacts.

The structure of echovirus type 12 bound to a two-domain fragment of its cellular attachment protein decay-accelerating factor (CD 55)

Echovirus type 12 (EV12), an enterovirus of the Picornaviridae family, uses the complement regulator, decay-accelerating factor (DAF, CD55) as a cellular receptor. We have calculated a three-dimensional reconstruction of EV12 bound to a fragment of DAF, consisting of short consensus repeat domains 3 and 4, from cryo-negative stain electron microscopy data (EMD #1057). This shows that, as for an earlier reconstruction of the related echovirus type 7 bound to DAF, attachment is not within the viral canyon but occurs close to the two-fold symmetry axes. Despite this general similarity, our reconstruction reveals a receptor interaction that is quite different from that observed for EV7. Fitting of the crystallographic co-ordinates for DAF34 and EV11 into the reconstruction shows a close agreement between the crystal structure of the receptor fragment and the density for the virus-bound receptor, allowing unambiguous positioning of the receptor with respect to the virion (PDB #1UPN). Our finding that the mode of virus-receptor interaction in EV12 is distinct from that seen for EV7 raises interesting questions regarding the evolution and biological significance of the DAF-binding phenotype in these viruses.

Dung and nest surveys: estimating decay rates

1. Wildlife managers often require estimates of abundance. Direct methods of estimation are often impractical, especially in closed-forest environments, so indirect methods such as dung or nest surveys are increasingly popular. 2. Dung and nest surveys typically have three elements: surveys to estimate abundance of the dung or nests; experiments to estimate the production (defecation or nest construction) rate; and experiments to estimate the decay or disappearance rate. The last of these is usually the most problematic, and was the subject of this study. 3. The design of experiments to allow robust estimation of mean time to decay was addressed. In most studies to date, dung or nests have been monitored until they disappear. Instead, we advocate that fresh dung or nests are located, with a single follow-up visit to establish whether the dung or nest is still present or has decayed. 4. Logistic regression was used to estimate probability of decay as a function of time, and possibly of other covariates. Mean time to decay was estimated from this function. 5. Synthesis and applications. Effective management of mammal populations usually requires reliable abundance estimates. The difficulty in estimating abundance of mammals in forest environments has increasingly led to the use of indirect survey methods, in which abundance of sign, usually dung (e.g. deer, antelope and elephants) or nests (e.g. apes), is estimated. Given estimated rates of sign production and decay, sign abundance estimates can be converted to estimates of animal abundance. Decay rates typically vary according to season, weather, habitat, diet and many other factors, making reliable estimation of mean time to decay of signs present at the time of the survey problematic. We emphasize the need for retrospective rather than prospective rates, propose a strategy for survey design, and provide analysis methods for estimating retrospective rates.

Coxsackievirus B3-associated myocardial pathology and viral load reduced by recombinant soluble human decay-accelerating factor in mice

Coxsackievirus B3 (CVB3) infection can result in myocarditis, which in turn may lead to a protracted immune response and subsequent dilated cardiomyopathy. Human decay-accelerating factor (DAF), a binding receptor for CVB3, was synthesized as a soluble IgG1-Fc fusion protein (DAF-Fc). In vitro, DAF-Fc was able to inhibit complement activity and block infection by CVB3, although blockade of infection varied widely among strains of CVB3. To determine the effects of DAF-Fc in vivo, 40 adolescent A/J mice were infected with a myopathic strain of CVB3 and given DAF-Fc treatment 3 days before infection, during infection, or 3 days after infection; the mice were compared with virus alone and sham-infected animals. Sections of heart, spleen, kidney, pancreas, and liver were stained with hematoxylin and eosin and submitted to in situ hybridization for both positive-strand and negative-strand viral RNA to determine the extent of myocarditis and viral infection, respectively. Salient histopathologic features, including myocardial lesion area, cell death, calcification and inflammatory cell infiltration, pancreatitis, and hepatitis were scored without knowledge of the experimental groups. DAF-Fc treatment of mice either preceding or concurrent with CVB3 infection resulted in a significant decrease in myocardial lesion area and cell death and a reduction in the presence of viral RNA. All DAF-Fc treatment groups had reduced infectious CVB3 recoverable from the heart after infection. DAF-Fc may be a novel therapeutic agent for active myocarditis and acute dilated cardiomyopathy if given early in the infectious period, although more studies are needed to determine its mechanism and efficacy.

Excited states of nitro-polypyridine metal complexes and their ultrafast decay. Time-resolved IR absorption, spectroelectrochemistry, and TD-DFT calculations of fac-[Re(Cl)(CO)3(5-Nitro-1,10-phenanthroline)]

The lowest absorption band of fac-[Re(Cl)(CO)(3)(5-NO2-phen)] encompasses two close-lying MLCT transitions. The lower one is directed to LUMO, which is heavily localized on the NO2 group. The UV-vis absorption spectrum is well accounted for by TD-DFT (G03/PBEPBE1/CPCM), provided that the solvent, MeCN, is included in the calculations. Near-UV excitation of fac-[Re(Cl)(CO)(3)(5-NO2-phen)] populates a triplet metal to ligand charge-transfer excited state, (MLCT)-M-3, that was characterized by picosecond time-resolved IR spectroscopy. Large positive shifts of the v(CO) bands upon excitation (+70 cm(-1) for the A'(1) band) signify a very large charge separation between the Re(Cl)(CO)3 unit and the 5-NO2-phen ligand. Details of the excited-state character are revealed by TD-DFT calculated changes of electron density distribution. Experimental excited-state v(CO) wavenumbers agree well with those calculated by DFT. The (MLCT)-M-3 state decays with a ca. 10 ps lifetime (in MeCN) into another transient species, that was identified by TRIR and TD-DFT calculations as an intraligand (3)n pi* excited state, whereby the electron density is excited from the NO2 oxygen lone pairs to the pi* system of 5-NO2-phen. This state is short-lived, decaying to the ground state with a similar to 30 ps lifetime. The presence of an n pi* state seems to be the main factor responsible for the lack of emission and the very short lifetimes of 3 MLCT states seen in all d(6)-metal complexes of nitro-polypyridyl ligands. Localization of the excited electron density in the lowest (MLCT)-M-3 states parallels localization of the extra electron in the reduced state that is characterized by a very small negative shift of the v(CO) IR bands (-6 cm(-1) for A'(1)) but a large downward shift of the v(s)(NO2) IR band. The Re-Cl bond is unusually stable toward reduction, whereas the Cl ligand is readily substituted upon oxidation.