Insights into the diurnal cycle of global Earth outgoing radiation using a numerical weather prediction model

A globally complete, high temporal resolution and multiple-variable approach is employed to analyse the diurnal cycle of Earth’s outgoing energy flows. This is made possible via the use of Met Office model output for September 2010 that is assessed alongside regional satellite observations throughout. Principal component analysis applied to the longwave component of modelled outgoing radiation reveals dominant diurnal patterns related to land surface heating and convective cloud development, respectively explaining 68.5 and 16.0% of the variance at the global scale. The total variance explained by these first two patterns is markedly less than previous regional estimates from observations, and this analysis suggests that around half of the difference relates to the lack of global coverage in the observations. The first pattern is strongly and simultaneously coupled to the land surface temperature diurnal variations. The second pattern is strongly coupled to the cloud water content and height diurnal variations, but lags the cloud variations by several hours. We suggest that the mechanism con- trolling the delay is a moistening of the upper troposphere due to the evaporation of anvil cloud. The shortwave component of modelled outgoing radiation, analysed in terms of albedo, exhibits a very dominant pattern explaining 88.4 % of the variance that is related to the angle of incoming solar radiation, and a second pattern explaining 6.7 % of the variance that is related to compensating effects from convective cloud development and marine stratocumulus cloud dissipation. Similar patterns are found in regional satellite observations, but with slightly different timings due to known model biases. The first pattern is controlled by changes in surface and cloud albedo, and Rayleigh and aerosol scattering. The second pattern is strongly coupled to the diurnal variations in both cloud water content and height in convective regions but only cloud water content in marine stratocumulus regions, with substantially shorter lag times compared with the longwave counterpart. This indicates that the shortwave radiation response to diurnal cloud development and dissipation is more rapid, which is found to be robust in the regional satellite observations. These global, diurnal radiation patterns and their coupling with other geophysical variables demonstrate the process-level understanding that can be gained using this approach and highlight a need for global, diurnal observing systems for Earth outgoing radiation in the future

The Sinbad retrotransposon from the genome of the human blood fluke, Schistosoma mansoni, and the distribution of related Pao-like elements

BACKGROUND: Of the major families of long terminal repeat (LTR) retrotransposons, the Pao/BEL family is probably the least well studied. It is becoming apparent that numerous LTR retrotransposons and other mobile genetic elements have colonized the genome of the human blood fluke, Schistosoma mansoni. RESULTS: A proviral form of Sinbad, a new LTR retrotransposon, was identified in the genome of S. mansoni. Phylogenetic analysis indicated that Sinbad belongs to one of five discreet subfamilies of Pao/BEL like elements. BLAST searches of whole genomes and EST databases indicated that members of this clade occurred in species of the Insecta, Nematoda, Echinodermata and Chordata, as well as Platyhelminthes, but were absent from all plants, fungi and lower eukaryotes examined. Among the deuterostomes examined, only aquatic species harbored these types of elements. All four species of nematode examined were positive for Sinbad sequences, although among insect and vertebrate genomes, some were positive and some negative. The full length, consensus Sinbad retrotransposon was 6,287 bp long and was flanked at its 5'- and 3'-ends by identical LTRs of 386 bp. Sinbad displayed a triple Cys-His RNA binding motif characteristic of Gag of Pao/BEL-like elements, followed by the enzymatic domains of protease, reverse transcriptase (RT), RNAseH, and integrase, in that order. A phylogenetic tree of deduced RT sequences from 26 elements revealed that Sinbad was most closely related to an unnamed element from the zebrafish Danio rerio and to Saci-1, also from S. mansoni. It was also closely related to Pao from Bombyx mori and to Ninja of Drosophila simulans. Sinbad was only distantly related to the other schistosome LTR retrotransposons Boudicca, Gulliver, Saci-2, Saci-3, and Fugitive, which are gypsy-like. Southern hybridization and bioinformatics analyses indicated that there were about 50 copies of Sinbad in the S. mansoni genome. The presence of ESTs representing transcripts of Sinbad in numerous developmental stages of S. mansoni along with the identical 5'- and 3'-LTR sequences suggests that Sinbad is an active retrotransposon. CONCLUSION: Sinbad is a Pao/BEL type retrotransposon from the genome of S. mansoni. The Pao/BEL group appears to be comprised of at least five discrete subfamilies, which tend to cluster with host species phylogeny. Pao/BEL type elements appear to have colonized only the genomes of the Animalia. The distribution of these elements in the Ecdysozoa, Deuterostomia, and Lophotrochozoa is discontinuous, suggesting horizontal transmission and/or efficient elimination of Pao-like mobile genetic elements from some genomes

Scaling Behaviour and Complexity of the Portevin-Le Chatelier Effect

The plastic deformation of dilute alloys is often accompanied by plastic instabilities due to dynamic strain aging and dislocation interaction. The repeated breakaway of dislocations from and their recapture by solute atoms leads to stress serrations and localized strain in the strain controlled tensile tests, known as the Portevin-Le Chatelier (PLC) effect. In this present work, we analyse the stress time series data of the observed PLC effect in the constant strain rate tensile tests on Al-2.5%Mg alloy for a wide range of strain rates at room temperature. The scaling behaviour of the PLC effect was studied using two complementary scaling analysis methods: the finite variance scaling method and the diffusion entropy analysis. From these analyses we could establish that in the entire span of strain rates, PLC effect showed Levy walk property. Moreover, the multiscale entropy analysis is carried out on the stress time series data observed during the PLC effect to quantify the complexity of the distinct spatiotemporal dynamical regimes. It is shown that for the static type C band, the entropy is very low for all the scales compared to the hopping type B and the propagating type A bands. The results are interpreted considering the time and length scales relevant to the effect.Comment: 35 pages, 6 figure

Granulin Secreted by the Food-Borne Liver Fluke

The liver fluke Opisthorchis viverrini is a food-borne, zoonotic pathogen endemic to Thailand and adjacent countries in Southeast Asia. The adult developmental stage of the O. viverrini parasite excretes and secretes numerous proteins within the biliary tract including the gall bladder. Lesions caused by the feeding activities of the liver fluke represent wounds that undergo protracted cycles of healing and re-injury during chronic infection, which can last for decades. Components of the excretory/secretory (ES) complement released by the worms capably drive proliferation of bile duct epithelial cells and are implicated in establishing the oncogenic milieu that leads to bile duct cancer, cholangiocarcinoma. An ES protein, the secreted granulin-like growth factor termed Ov-GRN-1, accelerates wound resolution in mice and in vitro. To investigate angiogenesis (blood vessel development) that may contribute to wound healing promoted by liver fluke granulin and, by implication, to carcinogenesis during chronic opisthorchiasis, we employed an in vitro tubule formation assay (TFA) where human umbilical vein endothelial cells were grown on gelled basement matrix. Ten and 40 nM Ov-GRN-1 significantly stimulated angiogenesis as monitored by cellular proliferation and by TFA in real time. This demonstration of potent angiogenic property of Ov-GRN-1 bolsters earlier reports on the therapeutic potential for chronic non-healing wounds of diabetics, tobacco users, and the elderly and, in addition, showcases another of the hallmark of cancer characteristic of this carcinogenic liver fluke

Electroporation Facilitates Introduction of Reporter Transgenes and Virions into Schistosome Eggs

The genome sequences of two of the three major species of schistosomes are now available. Molecular tools are needed to determine the importance of these new genes. With this in mind, we investigated introduction of reporter transgenes into schistosome eggs, with the longer-term aim of manipulation of schistosome genes and gene functions. The egg is a desirable developmental stage for genome manipulation, not least because it contains apparently accessible germ cells. Introduction of transgenes into the germ cells of schistosome eggs might result in transgenic schistosomes. However, the egg is surrounded by a thick shell which might block access to entry of transgenes. We cultured eggs in the presence of three types of reporter transgenes of increasing molecular size, and in addition we tried to produce transient holes in the eggs by electroporation to investigate whether the transgenes would more easily enter the eggs. Electroporation of eggs appeared to allow entry of two larger types of transgenes into cultured schistosome eggs, messenger RNA encoding firefly luciferase, and retroviral virions. We anticipate that this approach, electroporation of transgenes into schistosome eggs, will facilitate genetic manipulation of schistosomes for investigating the importance of schistosome genes and gene products as new intervention targets

The contrasting roles of water and dust in controlling daily variations in radiative heating of the summertime Saharan heat low

The summertime Sahara heat low (SHL) is a key component of the West African monsoon (WAM) system. Considerable uncertainty remains over the relative roles of water vapour and dust aerosols in controlling the radiation budget over the Sahara and therefore our ability to explain variability and trends in the SHL, and in turn, the WAM. Here, new observations from Fennec supersite-1 in the central Sahara during June 2011 and June 2012, together with satellite retrievals from GERB, are used to quantify how total column water vapour (TCWV) and dust aerosols (from aerosol optical depth, AOD) control day-to-day variations in energy balance in both observations and ECWMF reanalyses (ERA-I). The data show that the earth-atmosphere system is radiatively heated in June 2011 and 2012. Although the empirical analysis of observational data cannot completely disentangle the roles of water vapour, clouds and dust, the analysis demonstrates that TCWV provides a far stronger control on TOA net radiation, and so the net heating of the earth-atmosphere system, than AOD does. In contrast, variations in dust provide a much stronger control on surface heating, but the decreased surface heating associated with dust is largely compensated by increased atmospheric heating, and so dust control on net TOA radiation is weak. Dust and TCWV are both important for direct atmospheric heating. ERA-I, which assimilated radiosondes from the Fennec campaign, captures the control of TOA net flux by TCWV, with a positive correlation (r = 0.6) between observed and modelled TOA net radiation, despite the use of a monthly dust climatology in ERA-I that cannot capture the daily variations in dustiness. Variations in surface net radiation, and so the vertical profile of radiative heating, are not captured in ERA-I, since it does not capture variations in dust. Results show that ventilation of the SHL by cool moist air leads to a radiative warming, stabilising the SHL with respect to such perturbations. It is known that models struggle to capture the advective moistening of the SHL, especially that associated with mesoscale convective systems. Our results show that the typical model errors in Saharan water vapour will lead to substantial errors in the modelled TOA energy balance (tens of W m−2), which will lead to errors in both the SHL and the WAM

Characterization of dust emission from alluvial sources using aircraft observations and high-resolution modeling

International audienceWe investigate mineral dust emission from alluvial sediments within the upland region in northern Mauritania in the vicinity of a decaying nocturnal low-level jet (LLJ). For the first time, the impact of valleys that are embedded in a rather homogeneous surrounding is investigated with regard to their role as dust source. Measures for local atmospheric dust burden were retrieved from airborne observations, satellite observations, and model simulations and analyzed in order to provide complementary information at different horizontal scales. Observations by the LEANDRE Nouvelle Generation backscatter lidar system flying aboard the French Falcon 20 aircraft were taken along five parallel flight legs perpendicular to the orientation of the main valley system dominating the topography of the study area. Results from a comparison of lidar-derived extinction coefficients with topography and aerial photographs confirm the relevance of (1) alluvial sediments at the valley bottoms as a dust source, and (2) the break-down of the nocturnal LLJ as a trigger for dust emission in this region. An evaluation of the AROME regional model, forecasting dust at high resolution (5 km grid), points toward an under-representation of alluvial dust sources in this region. This is also evident from simulations by the MesoNH research model. Although MesoNH simulations show higher dust loadings than AROME, which are more comparable to the observations, both models underestimate the dust concentrations within the boundary layer compared to lidar observations. A sensitivity study on the impact of horizontal grid spacing (5 km versus 1 km) highlights the importance of spatial resolution on simulated dust loadings

High order amplitude equation for steps on creep curve

We consider a model proposed by one of the authors for a type of plastic instability found in creep experiments which reproduces a number of experimentally observed features. The model consists of three coupled non-linear differential equations describing the evolution of three types of dislocations. The transition to the instability has been shown to be via Hopf bifurcation leading to limit cycle solutions with respect to physically relevant drive parameters. Here we use reductive perturbative method to extract an amplitude equation of up to seventh order to obtain an approximate analytic expression for the order parameter. The analysis also enables us to obtain the bifurcation (phase) diagram of the instability. We find that while supercritical bifurcation dominates the major part of the instability region, subcritical bifurcation gradually takes over at one end of the region. These results are compared with the known experimental results. Approximate analytic expressions for the limit cycles for different types of bifurcations are shown to agree with their corresponding numerical solutions of the equations describing the model. The analysis also shows that high order nonlinearities are important in the problem. This approach further allows us to map the theoretical parameters to the experimentally observed macroscopic quantities.Comment: LaTex file and eps figures; Communicated to Phys. Rev.

Schistosoma mansoni α-N-acetylgalactosaminidase (SmNAGAL) regulates coordinated parasite movement and egg production

α-galactosidase (α-GAL) and α-N-acetylgalactosaminidase (α-NAGAL) are two glycosyl hydrolases responsible for maintaining cellular homeostasis by regulating glycan substrates on proteins and lipids. Mutations in the human genes encoding either enzyme lead to neurological and neuromuscular impairments seen in both Fabry- and Schindler/Kanzaki- diseases. Here, we investigate whether the parasitic blood fluke Schistosoma mansoni, responsible for the neglected tropical disease schistosomiasis, also contains functionally important α-GAL and α-NAGAL proteins. As infection, parasite maturation and host interactions are all governed by carefully-regulated glycosylation processes, inhibiting S. mansoni’s α-GAL and α-NAGAL activities could lead to the development of novel chemotherapeutics. Sequence and phylogenetic analyses of putative α-GAL/α-NAGAL protein types showed Smp_089290 to be the only S. mansoni protein to contain the functional amino acid residues necessary for α-GAL/α-NAGAL substrate cleavage. Both α-GAL and α-NAGAL enzymatic activities were higher in females compared to males (p α-GAL), which was consistent with smp_089290’s female biased expression. Spatial localisation of smp_089290 revealed accumulation in parenchymal cells, neuronal cells, and the vitellaria and mature vitellocytes of the adult schistosome. siRNA-mediated knockdown (>90%) of smp_089290 in adult worms significantly inhibited α-NAGAL activity when compared to control worms (siLuc treated males, p<0.01; siLuc treated females, p<0.05). No significant reductions in α-GAL activities were observed in the same extracts. Despite this, decreases in α-NAGAL activities correlated with a significant inhibition in adult worm motility as well as in egg production. Programmed CRISPR/Cas9 editing of smp_089290 in adult worms confirmed the egg reduction phenotype. Based on these results, Smp_089290 was determined to act predominantly as an α-NAGAL (hereafter termed SmNAGAL) in schistosome parasites where it participates in coordinating movement and oviposition processes. Further characterisation of SmNAGAL and other functionally important glycosyl hydrolases may lead to the development of a novel anthelmintic class of compounds