Tropical cyclones in a T159 Resolution Global Climate Model: comparison with observations and re-analyses

Tropical cyclones have been investigated in a T159 version of the MPI ECHAM5 climate model using a novel technique to diagnose the evolution of the 3-dimensional vorticity structure of tropical cyclones, including their full life cycle from weak initial vortex to their possible extra-tropical transition. Results have been compared with reanalyses (ERA40 and JRA25) and observed tropical storms during the period 1978-1999 for the Northern Hemisphere. There is no indication of any trend in the number or intensity of tropical storms during this period in ECHAM5 or in re-analyses but there are distinct inter-annual variations. The storms simulated by ECHAM5 are realistic both in space and time, but the model and even more so the re-analyses, underestimate the intensities of the most intense storms (in terms of their maximum wind speeds). There is an indication of a response to ENSO with a smaller number of Atlantic storms during El Niño in agreement with previous studies. The global divergence circulation responds to El Niño by setting up a large-scale convergence flow, with the center over the central Pacific with enhanced subsidence over the tropical Atlantic. At the same time there is an increase in the vertical wind shear in the region of the tropical Atlantic where tropical storms normally develop. There is a good correspondence between the model and ERA40 except that the divergence circulation is somewhat stronger in the model. The model underestimates storms in the Atlantic but tends to overestimate them in the Western Pacific and in the North Indian Ocean. It is suggested that the overestimation of storms in the Pacific by the model is related to an overly strong response to the tropical Pacific SST anomalies. The overestimation in 2 the North Indian Ocean is likely to be due to an over prediction in the intensity of monsoon depressions, which are then classified as intense tropical storms. Nevertheless, overall results are encouraging and will further contribute to increased confidence in simulating intense tropical storms with high-resolution climate models.

Equatorial Kelvin waves as revealed by EOS Microwave Limb Sounder observations and European Centre for Medium-Range Weather Forecasts analyses: Evidence for slow Kelvin waves of zonal wave number 3

[1] Temperature and ozone observations from the Microwave Limb Sounder (MLS) on the EOS Aura satellite are used to study equatorial wave activity in the autumn of 2005. In contrast to previous observations for the same season in other years, the temperature anomalies in the middle and lower tropical stratosphere are found to be characterized by a strong wave-like eastward progression with zonal wave number equal to 3. Extended empirical orthogonal function (EOF) analysis reveals that the wave 3 components detected in the temperature anomalies correspond to a slow Kelvin wave with a period of 8 days and a phase speed of 19 m/s. Fluctuations associated with this Kelvin wave mode are also apparent in ozone profiles. Moreover, as expected by linear theory, the ozone fluctuations observed in the lower stratosphere are in phase with the temperature perturbations, and peak around 20–30 hPa where the mean ozone mixing ratios have the steepest vertical gradient. A search for other Kelvin wave modes has also been made using both the MLS observations and the analyses from one experiment where MLS ozone profiles are assimilated into the European Centre for Medium-Range Weather Forecasts (ECMWF) data assimilation system via a 6-hourly 3D var scheme. Our results show that the characteristics of the wave activity detected in the ECMWF temperature and ozone analyses are in good agreement with MLS data.

Immersive Projection for biochemical pattern matching

In all biological processes, protein molecules and other small molecules interact to function and form transient macromolecular complexes. This interaction of two or more molecules can be described by a docking event. Docking is an important phase for structure-based drug design strategies, as it can be used as a method to simulate protein-ligand interactions. Various docking programs exist that allow automated docking, but most of them have limited visualization and user interaction. It would be advantageous if scientists could visualize the molecules participating in the docking process, manipulate their structures and manually dock them before submitting the new conformations to an automated docking process in an immersive environment, which can help stimulate the design/docking process. This also could greatly reduce docking time and resources. To achieve this, we propose a new virtual modelling/docking program, whereby the advantages of virtual modelling programs and the efficiency of the algorithms in existing docking programs will be merged.

Microbial perchlorate reduction: A precise laboratory determination of the chlorine isotope fractionation and its possible biochemical basis

Perchlorate-reducing bacteria fractionate chlorine stable isotopes giving a powerful approach to monitor the extent of microbial consumption of perchlorate in contaminated sites undergoing remediation or natural perchlorate containing sites. This study reports the full experimental data and methodology used to re-evaluate the chlorine isotope fractionation of perchlorate reduction in duplicate culture experiments of Azospira suillum strain PS at 37 degrees C (Delta Cl-37(Cr)--ClO4-) previously reported, without a supporting data set by Coleman et al. [Coleman, M.L., Ader, M., Chaudhuri, S., Coates,J.D., 2003. Microbial Isotopic Fractionation of Perchlorate Chlorine. Appl. Environ. Microbiol. 69, 4997-5000] in a reconnaissance study, with the goal of increasing the accuracy and precision of the isotopic fractionation determination. The method fully described here for the first time, allows the determination of a higher precision Delta Cl-37(Cl)--ClO4- value, either from accumulated chloride content and isotopic composition or from the residual perchlorate content and isotopic composition. The result sets agree perfectly, within error, giving average Delta Cl-37(Cl)--ClO4- = -14.94 +/- 0.15%omicron. Complementary use of chloride and perchlorate data allowed the identification and rejection of poor quality data by applying mass and isotopic balance checks. This precise Delta Cl-37(Cl)--ClO4-, value can serve as a reference point for comparison with future in situ or microcosm studies but we also note its similarity to the theoretical equilibrium isotopic fractionation between a hypothetical chlorine species of redox state +6 and perchlorate at 37 degrees C and suggest that the first electron transfer during perchlorate reduction may occur at isotopic equilibrium between art enzyme-bound chlorine and perchlorate. (C) 2008 Elsevier B.V. All rights reserved.

Accumulated metal speciation in earthworm populations with multi-generational exposure to metalliferous soils: cell fractionation and high energy synchrotron analyses

Predicting metal bioaccumulation and toxicity in soil organisms is complicated by site-specific biotic and abiotic parameters. In this study we exploited tissue fractionation and digestion techniques, combined with X-ray absorption spectroscopy (XAS), to investigate the whole-body and subcellular distributions, ligand affinities, and coordination chemistry of accumulated Pb and Zn in field populations of the epigeic earthworm Lumbricus rubellus inhabiting three contrasting metalliferous and two unpolluted soils. Our main findings were (i) earthworms were resident in soils with concentrations of Pb and Zn ranging from 1200 to 27 000 mg kg(-1) and 200 to 34 000 mg kg(-1), respectively; (ii) Pb and Zn primarily accumulated in the posterior alimentary canal in nonsoluble subcellular fractions of earthworms; (iii) site-specific differences in the tissue and subcellular partitioning profiles of populations were observed, with earthworms from a calcareous site partitioning proportionally more Pb to their anterior body segments and Zn to the chloragosome-rich subcellular fraction than their acidic-soil inhabiting counterparts; (iv) XAS indicated that the interpopulation differences in metal partitioning between organs were not accompanied by qualitative differences in ligand-binding speciation, because crystalline phosphate-containing pyromorphite was a predominant chemical species in the whole-worm tissues of all mine soil residents. Differences in metal (Pb, Zn) partitioning at both organ and cellular levels displayed by field populations with protracted histories of metal exposures may reflect their innate ecophysiological responses to essential edaphic variables, such as Ca2+ status. These observations are highly significant in the challenging exercise of interpreting holistic biomarker data delivered by "omic" technologies.

Soil geochemical analyses as an indication of metal working at the excavation of a house in the Roman City at Silchester (UK)

Silchester is the site of a major late Iron Age and Roman town (Calleva Atrebatum), situated in northern Hampshire (England (UK)) and occupied between the late first century BC and the fifth or sixth century AD. Extensive evidence of the nature of the buildings and the plan of the town was obtained from excavations undertaken between 1890 and 1909. The purpose of this study was to use soil geochemical analyses to reinforce the archaeological evidence particularly with reference to potential metal working at the site. Soil analysis has been used previously to distinguish different functions or land use activity over a site and to aid identification and interpretation of settlement features (Entwistle et al., 2000). Samples were taken from two areas of the excavation on a 1-metre grid. Firstly from an area of some 500 square metres from contexts of late first/early second century AD date throughout the entirety of a large 'town house' (House 1) from which there was prima facie evidence of metalworking.

Exploring other childhoods through quantitative secondary analyses of large scale surveys: opportunities and challenges for children's geographers

This paper considers the potential contribution of secondary quantitative analyses of large scale surveys to the investigation of 'other' childhoods. Exploring other childhoods involves investigating the experience of young people who are unequally positioned in relation to multiple, embodied, identity locations, such as (dis)ability, 'class', gender, sexuality, ethnicity and race. Despite some possible advantages of utilising extensive databases, the paper outlines a number of methodological problems with existing surveys which tend to reinforce adultist and broader hierarchical social relations. It is contended that scholars of children's geographies could overcome some of these problematic aspects of secondary data sources by endeavouring to transform the research relations of large scale surveys. Such endeavours would present new theoretical, ethical and methodological complexities, which are briefly considered.

A record of Holocene climate change from lake geochemical analyses in southeastern Arabia

Lacustrine sediments from southeastern Arabia reveal variations in lake level corresponding to changes in the strength and duration of Indian Ocean Monsoon (IOM) summer rainfall and winter cyclonic rainfall. The late glacial/Holocene transition of the region was characterised by the development of mega-linear dunes. These dunes became stabilised and vegetated during the early Holocene and interdunal lakes formed in response to the incursion of the IOM at approximately 8500 cal yr BP with the development of C3 dominated savanna grasslands. The IOM weakened ca. 6000 cal yr BP with the onset of regional aridity, aeolian sedimentation and dune reactivation and accretion. Despite this reduction in precipitation, the take was maintained by winter dominated rainfall. There was a shift to drier adapted C4 grasslands across the dune field. Lake sediment geochemical analyses record precipitation minima at 8200, 5000 and 4200 cal yr BP that coincide with Bond events in the North Atlantic. A number of these events correspond with changes in cultural periods, suggesting that climate was a key mechanism affecting human occupation and exploitation of this region. (c) 2006 University of Washington. All rights reserved.

The ASSET intercomparison of ozone analyses: method and first results

This paper aims to summarise the current performance of ozone data assimilation (DA) systems, to show where they can be improved, and to quantify their errors. It examines 11 sets of ozone analyses from 7 different DA systems. Two are numerical weather prediction (NWP) systems based on general circulation models (GCMs); the other five use chemistry transport models (CTMs). The systems examined contain either linearised or detailed ozone chemistry, or no chemistry at all. In most analyses, MIPAS (Michelson Interferometer for Passive Atmospheric Sounding) ozone data are assimilated; two assimilate SCIAMACHY (Scanning Imaging Absorption Spectrometer for Atmospheric Chartography) observations instead. Analyses are compared to independent ozone observations covering the troposphere, stratosphere and lower mesosphere during the period July to November 2003. Biases and standard deviations are largest, and show the largest divergence between systems, in the troposphere, in the upper-troposphere/lower-stratosphere, in the upper-stratosphere and mesosphere, and the Antarctic ozone hole region. However, in any particular area, apart from the troposphere, at least one system can be found that agrees well with independent data. In general, none of the differences can be linked to the assimilation technique (Kalman filter, three or four dimensional variational methods, direct inversion) or the system (CTM or NWP system). Where results diverge, a main explanation is the way ozone is modelled. It is important to correctly model transport at the tropical tropopause, to avoid positive biases and excessive structure in the ozone field. In the southern hemisphere ozone hole, only the analyses which correctly model heterogeneous ozone depletion are able to reproduce the near-complete ozone destruction over the pole. In the upper-stratosphere and mesosphere (above 5 hPa), some ozone photochemistry schemes caused large but easily remedied biases. The diurnal cycle of ozone in the mesosphere is not captured, except by the one system that includes a detailed treatment of mesospheric chemistry. These results indicate that when good observations are available for assimilation, the first priority for improving ozone DA systems is to improve the models. The analyses benefit strongly from the good quality of the MIPAS ozone observations. Using the analyses as a transfer standard, it is seen that MIPAS is similar to 5% higher than HALOE (Halogen Occultation Experiment) in the mid and upper stratosphere and mesosphere (above 30 hPa), and of order 10% higher than ozonesonde and HALOE in the lower stratosphere (100 hPa to 30 hPa). Analyses based on SCIAMACHY total column are almost as good as the MIPAS analyses; analyses based on SCIAMACHY limb profiles are worse in some areas, due to problems in the SCIAMACHY retrievals.

Phylogeny, function, and evolution of the cupins, a structurally conserved, functionally diverse superfamily of proteins

The cupin superfamily is a group of functionally diverse proteins that are found in all three kingdoms of life, Archaea, Eubacteria, and Eukaryota. These proteins have a characteristic signature domain comprising two histidine- containing motifs separated by an intermotif region of variable length. This domain consists of six beta strands within a conserved beta barrel structure. Most cupins, such as microbial phosphomannose isomerases (PMIs), AraC- type transcriptional regulators, and cereal oxalate oxidases (OXOs), contain only a single domain, whereas others, such as seed storage proteins and oxalate decarboxylases (OXDCs), are bi-cupins with two pairs of motifs. Although some cupins have known functions and have been characterized at the biochemical level, the majority are known only from gene cloning or sequencing projects. In this study, phylogenetic analyses were conducted on the conserved domain to investigate the evolution and structure/function relationships of cupins, with an emphasis on single- domain plant germin-like proteins (GLPs). An unrooted phylogeny of cupins from a wide spectrum of evolutionary lineages identified three main clusters, microbial PMIs, OXDCs, and plant GLPs. The sister group to the plant GLPs in the global analysis was then used to root a phylogeny of all available plant GLPs. The resulting phylogeny contained three main clades, classifying the GLPs into distinct subfamilies. It is suggested that these subfamilies correlate with functional categories, one of which contains the bifunctional barley germin that has both OXO and superoxide dismutase (SOD) activity. It is proposed that GLPs function primarily as SODs, enzymes that protect plants from the effects of oxidative stress. Closer inspection of the DNA sequence encoding the intermotif region in plant GLPs showed global conservation of thymine in the second codon position, a character associated with hydrophobic residues. Since many of these proteins are multimeric and enzymatically inactive in their monomeric state, this conservation of hydrophobicity is thought to be associated with the need to maintain the various monomer- monomer interactions. The type of structure-based predictive analysis presented in this paper is an important approach for understanding gene function and evolution in an era when genomes from a wide range of organisms are being sequenced at a rapid rate.

Use of fibrolytic enzymes to improve the nutritive value of ruminant diets - A biochemical and in vitro rumen degradation assessment

Two commercial enzyme products, Depol 40 (D) and Liquicell 2500 (L), were characterised from a biochemical standpoint and their potential to improve rumen degradation of forages was evaluated in vitro. Enzyme activities were determined at pH 5.5 and 39 degreesC. Analysis of the enzyme activities indicated that L contained higher xylanase and endoglucanase, but lower exoglucanase, pectinase and alpha-amylase activities than D. The Reading Pressure Technique (RPT) was used to investigate the effect of enzyme addition on the in vitro gas production (GP) and organic matter degradation (OMD) of alfalfa (Medicago sativa L.) stems and leaves. A completely randomised design with factorial arrangement of treatments was used. Both alfalfa fractions were untreated or treated with each enzyme at four levels, 20 h before incubation with rumen fluid. Each level of enzyme provided similar amounts of filter paper (D1, L1), endoglucanase (D2, L2), alpha-L-arabinofuranosidase (D3, L3) and xylanase units (D4, L4) per gram forage DM. Enzymes increased the initial OMD in both fractions, with improvements of up to 15% in leaves (D4) and 8% in stems (L2) after 12 h incubation. All enzyme treatments increased the extent of degradation (96 h incubation) in the leaf fractions, but only L2 increased final OMD in the stems. Direct hydrolysis of forage fractions during the pre-treatment period did not fully account for the magnitude of the increases in OMD, suggesting that the increase in rate of degradation was achieved through a combined effect of direct enzyme hydrolysis and synergistic action between the exogenous (applied) and endogenous (rumen) enzymes. (C) 2003 Elsevier Science B.V. All rights reserved.