Prevalence of mutations within the quinolone resistance-determining region of gyrA, gyrB, parC, and parE and association with antibiotic resistance in quinolone-resistant Salmonella enterica

Salmonella enterica isolates (n = 182) were examined for mutations in the quinolone resistance-determining region of gyrA, gyrB, parC, and parE. The frequency, location, and type of GyrA substitution varied with the serovar. Mutations were found in parC that encoded Thr57-Ser, Thr66-Ile, and Ser80-Arg substitutions. Mutations in the gyrB quinolone resistance-determining region were located at codon Tyr420-Cys or Arg437-Len. Novel mutations were also found in parE encoding Glu453-Gly, His461-Tyr, Ala498-Thr, Val512-Gly, and Ser518-Cys. Although it is counterintuitive, isolates with a mutation in both gyrA and parC were more susceptible to ciprofloxacin than were isolates with a mutation in gyrA alone.

Acid-base reactions between an acidic soil and plant residues

The elemental composition of residues of maize (Zea mays), sorghum (S. bicolor), groundnuts (Arachis hypogea), soya beans (Glycine max), leucaena (L. leucocephala), gliricidia (G. sepium), and sesbania (S. sesban) was determined as a basis for examining their alkalinity when incorporated into an acidic Zambian Ferralsol. Potential (ash) alkalinity, available alkalinity by titration to pH 4 and soluble alkalinity (16 It water extract titrated to pH 4) were measured. Potential alkalinity ranged from 3 73 (maize) to 1336 (groundnuts) mmol kg(-1) and was equivalent to the excess of their cation charge over inorganic anion charge. Available alkalinity was about half the potential alkalinity. Cations associated with organic anions are the source of alkalinity. About two thirds of the available alkalinity is soluble. Residue buffer curves were determined by titration with H2SO4 to pH 4. Soil buffer capacity measured by addition of NaOH was 12.9 mmol kg(-1) pH(-1). Soil and residue (10 g:0.25 g) were shaken in solution for 24 h and suspension pH values measured. Soil pH increased from 4.3 to between 4.6 (maize) and 5.2 (soyabean) and the amounts of acidity neutralized (calculated from the rise in pH and the soil buffer capacity) were between 3.9 and 11.5 mmol kg(-1), respectively. The apparent base contributions by the residues (calculated from the buffer curves and the fall in pH) ranged between 105 and 350 mmol kg(-1) of residue, equivalent to 2.6 and 8.8 mmol kg(-1) of soil, respectively. Therefore, in contact with soil acidity, more alkalinity becomes available than when in contact with H2SO4 solution. Available alkalinity (to pH 4) would be more than adequate to supply that which reacts with soil but soluble alkalinity would not. It was concluded that soil Al is able to displace cations associated with organic anions in the residues which are not displaced by H+, or that residue decomposition may have begun in the soil suspension releasing some of the non-available alkalinity. Soil and four of the residues were incubated for 100 days and changes in pH, NH4+ and NO3- concentrations measured. An acidity budget equated neutralized soil acidity with residue alkalinity and base or acid produced by N transformations. Most of the potential alkalinity of soyabean and leucaena had reacted after 14 days, but this only occurred after 100 days for gliricidia, and for maize only the available alkalinity reacted. For gliricidia and leucaena, residue alkalinity was primarily used to react with acidity produced by nitrification. Thus, the ability of residues to ameliorate acidity depends not only on their available and potential alkalinity but also on their potential to release mineral N. (C) 2004 Elsevier B.V. All rights reserved.

Characterization of the 23S and 5S rRNA genes and 23S-5S intergenic spacer region (ITS-2) of Photobacterium damselae

The 23S ribosomal RNA (rRNA) gene has been sequenced in strains of the fish pathogens Photobacterium damselae subsp. damselae (ATCC 33539) and subsp. piscicida (ATCC 29690), showing that 3 nucleotide positions are clearly different between subspecies. In addition, the 5S rRNA gene plus the intergenic spacer region between the 23S and 5S rRNA genes (ITS-2) were amplified, cloned and sequenced for the 2 reference strains as well as the field isolates RG91 (subsp. damselae) and DI21 (subsp. piscicida). A 100% similarity was found for the consensus 5S rRNA gene sequence in the 2 subspecies, although some microheterogeneity was detected as inter-cistronic variability within the same chromosome. Sequence analysis of the spacer region between the 23S and 5S rRNA genes revealed 2 conserved and 3 variable nucleotide sequence blocks, and 4 different modular organizations were found. The ITS-2 spacer region exhibited both inter-subspecies and inter-cistronic polymorphism, with a mosaic-like structure. The EMBL accession numbers for the 23S, 5S and ITS-2 sequences are: P. damselae subsp. piscicida 5S gene (AJ274379), P. damselae subsp. damselae 23S gene (Y18520), subsp. piscicida 23S gene (Y17901), R damselae subsp. piscicida ITS-2 (AJ250695, AJ250696), P. damselae subsp. damselae ITS-2 (AJ250697, AJ250698).

Vegetation and environmental dynamics in the southern Black Sea region since 18 kyr BP derived from the marine core 22-GC3

Sediments from the Black Sea, a region historically dominated by forests and steppe landscapes, are a valuable source of detailed information on the changes in regional terrestrial and aquatic environments at decadal to millennial scales. Here we present multi-proxy environmental records (pollen, dinoflagellate cysts, Ca, Ti and oxygen isotope data) from the uppermost 305 cm of the core 22-GC3 (42°13.53′N, 36°29.55′E) collected from a water depth of 838 m in the southern part of the Black Sea in 2007. The records span the last ~ 18 kyr (all ages are given in cal kyr BP). The pollen data reveal the dominance of the Artemisia-steppe in the region, suggesting rather dry/cold environments ~ 18–14.5 kyr BP. Warming/humidity increase during melt-water pulses (~ 16.1–14.5 kyr BP), indicated by δ18O records from the 22-GC3 core sediment and from the Sofular Cave stalagmite, is expressed in more negative δ13C values from the Sofular Cave, usually interpreted as the spreading of C3 plants. The records representing the interstadial complex (~ 14.5–12.9 kyr BP) show an increase in temperature and moisture, indicated by forest development, increased primary productivity and reduced surface run-off, whereas the switch from primary terrigenous to primary authigenic Ca origin occurs ~ 500 yr later. The Younger Dryas cooling is clearly demonstrated by more negative δ13C values from the Sofular Cave and a reduction of pines. The early Holocene (11.7–8.5 kyr BP) interval reveals relatively dry conditions compared to the mostly moist and warm middle Holocene (8.5–5 kyr BP), which is characterized by the establishment of the species-rich warm mixed and temperate deciduous forests in the low elevation belt, temperate deciduous beech-hornbeam forests in the middle and cool conifer forest in upper mountain belt. The border between the early and middle Holocene in the vegetation records coincides with the opening of the Mediterranean corridor at ~ 8.3 kyr BP, as indicated by a marked change in the dinocyst assemblages and in the sediment lithology. Changes in the pollen assemblages indicate a reduction in forest cover after ~ 5 kyr BP, which was likely caused by increased anthropogenic pressure on the regional vegetation.

Validity of the ice shelf water plume concept beneath Filchner-Ronne Ice Shelf

In winter, brine rejection from sea ice formation and export in the Weddell Sea, offshore of Filchner-Ronne Ice Shelf (FRIS), leads to the formation of High Salinity Shelf Water (HSSW). This dense water mass enters the cavity beneath FRIS by sinking southward down the sloping continental shelf towards the grounding line. Melting occurs when the HSSW encounters the ice shelf, and the meltwater released cools and freshens the HSSW to form a water mass known as Ice Shelf Water (ISW). If this ISW rises, the ‘ice pump’ is initiated (Lewis and Perkin, 1986), whereby the ascending ISW becomes supercooled and deposits marine ice at shallower locations due to the pressure increase in the in-situ freezing temperature. Sandh¨ager et al. (2004) were able to infer the thickness patterns of marine ice deposits at the base of FRIS (figure 1), so the primary aim of this work is to try to understand the ocean flows that determine these patterns. The plume model we use to investigate ISW flow is described fully by Holland and Feltham (accepted) so only a relatively brief outline is presented here. The plume is simulated by combining a parameterisation of ice shelf basal interaction and a multiplesize- class frazil dynamics model with an unsteady, depth-averaged reduced-gravity plume model. In the model an active region of ISW evolves above and within an expanse of stagnant ambient fluid, which is considered to be ice-free and has fixed profiles of temperature and salinity. The two main assumptions of the model are that there is a well-mixed layer underneath the ice shelf and that the ambient fluid outside the plume is stagnant with fixed properties. The topography of the ice shelf that the plume flows beneath is set to the FRIS ice shelf draft calculated by Sandh¨ager et al. (2004) masked with the grounding line from the Antarctic Digital Database (ADD Consortium, 2002). To initiate the plumes, we assume that the intrusion of dense HSSW initially causes melting at the points on the grounding line where the glaciological tributaries feeding FRIS go afloat.

Pollen-based reconstructions of biome distributions for Australia, Southeast Asia and the Pacific (SEAPAC region) at 0,6000 and 18,000 14C yr B.P.

Aim  This paper documents reconstructions of the vegetation patterns in Australia, Southeast Asia and the Pacific (SEAPAC region) in the mid-Holocene and at the last glacial maximum (LGM). Methods  Vegetation patterns were reconstructed from pollen data using an objective biomization scheme based on plant functional types. The biomization scheme was first tested using 535 modern pollen samples from 377 sites, and then applied unchanged to fossil pollen samples dating to 6000 ± 500 or 18,000 ± 1000 14C yr bp. Results  1. Tests using surface pollen sample sites showed that the biomization scheme is capable of reproducing the modern broad-scale patterns of vegetation distribution. The north–south gradient in temperature, reflected in transitions from cool evergreen needleleaf forest in the extreme south through temperate rain forest or wet sclerophyll forest (WSFW) and into tropical forests, is well reconstructed. The transitions from xerophytic through sclerophyll woodlands and open forests to closed-canopy forests, which reflect the gradient in plant available moisture from the continental interior towards the coast, are reconstructed with less geographical precision but nevertheless the broad-scale pattern emerges. 2. Differences between the modern and mid-Holocene vegetation patterns in mainland Australia are comparatively small and reflect changes in moisture availability rather than temperature. In south-eastern Australia some sites show a shift towards more moisture-stressed vegetation in the mid-Holocene with xerophytic woods/scrub and temperate sclerophyll woodland and shrubland at sites characterized today by WSFW or warm-temperate rain forest (WTRF). However, sites in the Snowy Mountains, on the Southern Tablelands and east of the Great Dividing Range have more moisture-demanding vegetation in the mid-Holocene than today. South-western Australia was slightly drier than today. The single site in north-western Australia also shows conditions drier than today in the mid-Holocene. Changes in the tropics are also comparatively small, but the presence of WTRF and tropical deciduous broadleaf forest and woodland in the mid-Holocene, in sites occupied today by cool-temperate rain forest, indicate warmer conditions. 3. Expansion of xerophytic vegetation in the south and tropical deciduous broadleaf forest and woodland in the north indicate drier conditions across mainland Australia at the LGM. None of these changes are informative about the degree of cooling. However the evidence from the tropics, showing lowering of the treeline and forest belts, indicates that conditions were between 1 and 9 °C (depending on elevation) colder. The encroachment of tropical deciduous broadleaf forest and woodland into lowland evergreen broadleaf forest implies greater aridity. Main conclusions  This study provides the first continental-scale reconstruction of mid-Holocene and LGM vegetation patterns from Australia, Southeast Asia and the Pacific (SEAPAC region) using an objective biomization scheme. These data will provide a benchmark for evaluation of palaeoclimate simulations within the framework of the Palaeoclimate Modelling Intercomparison Project.

Distribution and statistics of African mesoscale convective weather systems based on the ISCCP Meteosat imagery

This paper provides for the first time an objective short-term (8 yr) climatology of African convective weather systems based on satellite imagery. Eight years of infrared International Satellite Cloud Climatology Project-European Space Agency's Meteorological Satellite (ISCCP-Meteosat) satellite imagery has been analyzed using objective feature identification, tracking, and statistical techniques for the July, August, and September periods and the region of Africa and the adjacent Atlantic ocean. This allows various diagnostics to be computed and used to study the distribution of mesoscale and synoptic-scale convective weather systems from mesoscale cloud clusters and squall lines to tropical cyclones. An 8-yr seasonal climatology (1983-90) and the seasonal cycle of this convective activity are presented and discussed. Also discussed is the dependence of organized convection for this region, on the orography, convective, and potential instability and vertical wind shear using European Centre for Medium-Range Weather Forecasts reanalysis data.

Spatial and temporal scale issues in determining biomass burning regimes in Bolivia and Peru

ATSR-2 active fire data from 1996 to 2000, TRMM VIRS fire counts from 1998 to 2000 and burn scars derived from SPOT VEGETATION ( the Global Burnt Area 2000 product) were mapped for Peru and Bolivia to analyse the spatial distribution of burning and its intra- and inter-annual variability. The fire season in the region mainly occurs between May and October; though some variation was found between the six broad habitat types analysed: desert, grassland, savanna, dry forest, moist forest and yungas (the forested valleys on the eastern slope of the Andes). Increased levels of burning were generally recorded in ATSR-2 and TRMM VIRS fire data in response to the 1997/1998 El Nino, but in some areas the El Nino effect was masked by the more marked influences of socio-economic change on land use and land cover. There were differences between the three global datasets: ATSR-2 under-recorded fires in ecosystems with low net primary productivities. This was because fires are set during the day in this region and, when fuel loads are low, burn out before the ATSR-2 overpass in the region which is between 02.45 h and 03.30 h. TRMM VIRS was able to detect these fires because its overpasses cover the entire diurnal range on a monthly basis. The GBA2000 product has significant errors of commission (particularly areas of shadow in the well-dissected eastern Andes) and omission (in the agricultural zone around Santa Cruz, Bolivia and in north-west Peru). Particular attention was paid to biomass burning in high-altitude grasslands, where fire is an important pastoral management technique. Fires and burn scars from Landsat Thematic Mapper (TM) and Enhanced Thematic Mapper (ETM) data for a range of years between 1987 and 2000 were mapped for areas around Parque Nacional Rio Abiseo (Peru) and Parque Nacional Carrasco (Bolivia). Burn scars mapped in the grasslands of these two areas indicate far more burning had taken place than either the fires or the burn scars derived from global datasets. Mean scar sizes are smaller and have a smaller range in size between years the in the study area in Peru (6.6-7.1 ha) than Bolivia (16.9-162.5 ha). Trends in biomass burning in the two highland areas can be explained in terms of the changing socio-economic environments and impacts of conservation. The mismatch between the spatial scale of biomass burning in the high-altitude grasslands and the sensors used to derive global fire products means that an entire component of the fire regime in the region studied is omitted, despite its importance in the farming systems on the Andes.

Trace element geochemistry from the Birrimian metasediments of the Northern Region of Ghana

Trace element distributions in rock, soil and groundwater from of the Birrimian metasediments and granites located in the Northern Region of Ghana are described. High positive correlations are observed between selected major elements and trace metals (e.g. K2O and Rb, Al2O3 and V, Fe2O3 and V, and K2O and Y) in rocks and soils, and attributed to the presence of major source minerals. Ca and Sr were strongly correlated in groundwater, suggesting greater water-rock interaction. Low association of V with Fe is explained by (i) relatively higher mobility of V as against Fe; (ii) low Fe content in the parent rocks and (iii) variable sources of Fe and V.

Case-based analysis in user requirements modelling for knowledge construction

Context: Learning can be regarded as knowledge construction in which prior knowledge and experience serve as basis for the learners to expand their knowledge base. Such a process of knowledge construction has to take place continuously in order to enhance the learners’ competence in a competitive working environment. As the information consumers, the individual users demand personalised information provision which meets their own specific purposes, goals, and expectations. Objectives: The current methods in requirements engineering are capable of modelling the common user’s behaviour in the domain of knowledge construction. The users’ requirements can be represented as a case in the defined structure which can be reasoned to enable the requirements analysis. Such analysis needs to be enhanced so that personalised information provision can be tackled and modelled. However, there is a lack of suitable modelling methods to achieve this end. This paper presents a new ontological method for capturing individual user’s requirements and transforming the requirements onto personalised information provision specifications. Hence the right information can be provided to the right user for the right purpose. Method: An experiment was conducted based on the qualitative method. A medium size of group of users participated to validate the method and its techniques, i.e. articulates, maps, configures, and learning content. The results were used as the feedback for the improvement. Result: The research work has produced an ontology model with a set of techniques which support the functions for profiling user’s requirements, reasoning requirements patterns, generating workflow from norms, and formulating information provision specifications. Conclusion: The current requirements engineering approaches provide the methodical capability for developing solutions. Our research outcome, i.e. the ontology model with the techniques, can further enhance the RE approaches for modelling the individual user’s needs and discovering the user’s requirements.

'Fair trade gold': Antecedents, prospects and challenges

This paper critically examines the challenges with, and impacts of, adopting the models in place for fair trade agriculture in the artisanal gold mining sector. Over the past two years, an NGO-led 'fair trade gold' movement has surfaced, its crystallization fuelled by a burgeoning body of evidence that points to impoverished artisanal miners in developing countries receiving low payments for their gold, as well as working in hazardous and unsanitary conditions. Proponents of fair trade gold contest that increased interaction between artisanal miners and Western jewellers could facilitate the former receiving fairer prices for gold, accessing support services, and ultimately, improving their quality of life. In the case of sub-Saharan Africa, however, the gold being mined on an artisanal scale does not supply Western retailers as perhaps believed; it is rather an important source of foreign exchange, which host governments employ buyers to collect for their coffers. It is maintained here that if the underlying purpose of fair trade is to improve the livelihoods and well-being of subsistence producers in developing countries, then the models that have proved so successful in alleviating the hardships of agro-producers of 'tropical' commodities such as coffee, tea, bananas and cocoa, should be adapted to artisanal gold mining in sub-Saharan Africa. Campaigns promoting 'fair trade gold' in the region should view host governments, and not Western retailers, as the 'end consumer', and focus on improving governance at the grassroots, organizing informal operators into working cooperatives, and addressing complications with purchasing arrangements - all of which would go a long way toward improving the livelihoods of subsistence artisanal miners. A case study of Noyem, Ghana, the location of a sprawling illegal gold mining community, is presented, which magnifies these challenges further and provides perspective on how they can be overcome. (c) 2007 Elsevier Ltd. All rights reserved.