Abrasion control on dune colour: Muleshoe Dunes, SW USA

The Muleshoe Dunes, an east-west trending dunefield on the border separating Texas and New Mexico, consist of two distinct components: a white (carbonate rich) component and an overlying pink (quartz rich) component. The pink component exhibits significant spatial variation in redness. The reddest sands, in the western part of the dunefield, decrease in redness towards the east. This gradient is thought to result from abrasion of all iron-rich, red clay coating as the sediments were transported eastward by Late Quaternary aeolian processes. The effects of aeolian abrasion on the spectral signature and surface texture of the sediments were examined using laboratory abrasion experiments. Changes in spectral reflectance of abrasion samples from the laboratory were compared to field samples that were abraded naturally because of sediment transport. The changes resulting from increased time of abrasion are similar to those observed with increased distance downwind in the dunefield. These results suggest that downwind abrasion can explain the pattern of dune colour in the Muleshoe Dunes, although this does not preclude other possible causes. (C) 2008 Elsevier B.V. All rights reserved.

Geochemical mapping of carbonate sediments in the Makgadikgadi basin, Botswana using moderate resolution remote sensing data

This paper maps the carbonate geochemistry of the Makgadikgadi Pans region of northern Botswana from moderate resolution (500 m pixels) remotely sensed data, to assess the impact of various geomorphological processes on surficial carbonate distribution. Previous palaeo-environmental studies have demonstrated that the pans have experienced several highstands during the Quaternary, forming calcretes around shoreline embayments. The pans are also a significant regional source of dust, and some workers have suggested that surficial carbonate distributions may be controlled, in part, by wind regime. Field studies of carbonate deposits in the region have also highlighted the importance of fluvial and groundwater processes in calcrete formation. However, due to the large area involved and problems of accessibility, the carbonate distribution across the entire Makgadikgadi basin remains poorly understood. The MODIS instrument permits mapping of carbonate distribution over large areas; comparison with estimates from Landsat Thematic Mapper data show reasonable agreement, and there is good agreement with estimates from laboratory analysis of field samples. The results suggest that palaeo-lake highstands, reconstructed here using the SRTM 3 arc-second digital elevation model, have left behind surficial carbonate deposits, which can be mapped by the MODIS instrument. Copyright (c) 2006 John Wiley & Sons, Ltd.

Spectral properties, iron oxide content and provenance of Namib dune sands

This paper applies multispectral remote sensing techniques to map the Fe-oxide content over the entire Namib sand sea. Spectrometric analysis is applied to field samples to identify the reflectance properties of the dune sands which enable remotely sensed Fe-oxide mapping. The results indicate that the pattern of dune colour in the Namib sand sea arises from the mixing of at least two distinct sources of sand; a red component of high Fe-oxide content (present as a coating on the sand grains) which derives from the inland regions, particularly from major embayments into the Southern African escarpment; and a yellow coastal component of low Fe-oxide content which is brought into the area by northward-moving aeolian transport processes. These major provenances are separated by a mixing zone between 20 kin and 90 kin from the coast throughout the entire length of the sand sea. Previous workers have also recognised a third, fluvial, provenance, but the methodology applied here is not able to map this source as a distinct spectral component. (c) 2006 Elsevier B.V. All rights reserved.

Abrasion control on dune colour: Muleshoe Dunes, SW USA

The Muleshoe Dunes, an east-west trending dunefield on the border separating Texas and New Mexico, consist of two distinct components: a white (carbonate rich) component and an overlying pink (quartz rich) component. The pink component exhibits significant spatial variation in redness. The reddest sands, in the western part of the dunefield, decrease in redness towards the east. This gradient is thought to result from abrasion of all iron-rich, red clay coating as the sediments were transported eastward by Late Quaternary aeolian processes. The effects of aeolian abrasion on the spectral signature and surface texture of the sediments were examined using laboratory abrasion experiments. Changes in spectral reflectance of abrasion samples from the laboratory were compared to field samples that were abraded naturally because of sediment transport. The changes resulting from increased time of abrasion are similar to those observed with increased distance downwind in the dunefield. These results suggest that downwind abrasion can explain the pattern of dune colour in the Muleshoe Dunes, although this does not preclude other possible causes. (C) 2008 Elsevier B.V. All rights reserved.

Geochemical mapping of carbonate sediments in the Makgadikgadi basin, Botswana using moderate resolution remote sensing data

This paper maps the carbonate geochemistry of the Makgadikgadi Pans region of northern Botswana from moderate resolution (500 m pixels) remotely sensed data, to assess the impact of various geomorphological processes on surficial carbonate distribution. Previous palaeo-environmental studies have demonstrated that the pans have experienced several highstands during the Quaternary, forming calcretes around shoreline embayments. The pans are also a significant regional source of dust, and some workers have suggested that surficial carbonate distributions may be controlled, in part, by wind regime. Field studies of carbonate deposits in the region have also highlighted the importance of fluvial and groundwater processes in calcrete formation. However, due to the large area involved and problems of accessibility, the carbonate distribution across the entire Makgadikgadi basin remains poorly understood. The MODIS instrument permits mapping of carbonate distribution over large areas; comparison with estimates from Landsat Thematic Mapper data show reasonable agreement, and there is good agreement with estimates from laboratory analysis of field samples. The results suggest that palaeo-lake highstands, reconstructed here using the SRTM 3 arc-second digital elevation model, have left behind surficial carbonate deposits, which can be mapped by the MODIS instrument. Copyright (c) 2006 John Wiley & Sons, Ltd.

Spectral properties, iron oxide content and provenance of Namib dune sands

This paper applies multispectral remote sensing techniques to map the Fe-oxide content over the entire Namib sand sea. Spectrometric analysis is applied to field samples to identify the reflectance properties of the dune sands which enable remotely sensed Fe-oxide mapping. The results indicate that the pattern of dune colour in the Namib sand sea arises from the mixing of at least two distinct sources of sand; a red component of high Fe-oxide content (present as a coating on the sand grains) which derives from the inland regions, particularly from major embayments into the Southern African escarpment; and a yellow coastal component of low Fe-oxide content which is brought into the area by northward-moving aeolian transport processes. These major provenances are separated by a mixing zone between 20 kin and 90 kin from the coast throughout the entire length of the sand sea. Previous workers have also recognised a third, fluvial, provenance, but the methodology applied here is not able to map this source as a distinct spectral component. (c) 2006 Elsevier B.V. All rights reserved.

Molecular tools to investigate Rhizoctonia solani distribution in soil

Real-time PCR protocols were developed to detect and discriminate 11 anastomosis groups (AGs) of Rhizoctonia solani using ribosomal internal transcribed spacer (ITS) regions (AG-1-IA, AG-1-IC, AG-2-1, AG-2-2, AG-4HGI+II, AG-4HGIII, AG-8) or beta-tubulin (AG-3, AG-4HGII, AG-5 and AG-9) sequences. All real-time assays were target group specific, except AG-2-2, which showed a weak cross-reaction with AG-2tabac. In addition, methods were developed for the high throughput extraction of DNA from soil and compost samples. The DNA extraction method was used with the AG-2-1 assay and shown to be quantitative with a detection threshold of 10-7 g of R. solani per g of soil. A similar DNA extraction efficiency was observed for samples from three contrasting soil types. The developed methods were then used to investigate the spatial distribution of R. solani AG-2-1 in field soils. Soil from shallow depths of a field planted with Brassica oleracea tested positive for R. solani AG-2-1 more frequently than soil collected from greater depths. Quantification of R. solani inoculum in field samples proved challenging due to low levels of inoculum in naturally occurring soils. The potential uses of real-time PCR and DNA extraction protocols to investigate the epidemiology of R. solani are discussed.

Evaluation of a nucleoprotein-based enzyme-linked immunosorbent assay for the detection of antibodies against infectious bronchitis virus

As an immunogen of the coronavirus, the nucleoprotein (N) is a potential antigen for the serological monitoring of infectious bronchitis virus (IBV). In this report, recombinant N protein from the Beaudette strain of IBV was produced and purified from Escherichia coli as well as Sf9 ( insect) cells, and used for the coating of enzyme-linked immunosorbent assay ( ELISA) plates. The N protein produced in Sf9 cells was phosphorylated whereas N protein from E. coli was not. Our data indicated that N protein purified from E. coli was more sensitive to anti-IBV serum than the protein from Sf9 cells. The recombinant N protein did not react with the antisera to other avian pathogens, implying that it was specific in the recognition of IBV antibodies. In addition, the data from the detection of field samples and IBV strains indicated that using the recombinant protein as coating antigen could achieve an equivalent performance to an ELISA kit based on infected material extracts as a source of antigen(s). ELISAs based on recombinant proteins are safe ( no live virus), clean ( only virus antigens are present), specific ( single proteins can be used) and rapid ( to respond to new viral strains and strains that cannot necessarily be easily cultured).

Analysis of 16S rDNA sequences from pathogenic Leptospira serovars and use of single nucleotide polymorphisms for rapid speciation by D-HPLC

Leptospira have a worldwide distribution and include important zoonotic pathogens yet diagnosis and differentiation still tend to rely on traditional bacteriological and serological approaches. In this study a 1.3 kb fragment of the rrs gene (16S rDNA) was sequenced from a panel of 22 control strains, representing serovars within the pathogenic species Leptospira interrogans, Leptospira borgpetersenii, and Leptospira kirschneri, to identify single nucleotide polymorphisms (SNPs). These were identified in the 5' variable region of the 16S sequence and a 181 bp PCR fragment encompassing this region was used for speciation by Denaturing High Performance Liquid Chromatography (D-HPLC). This method was applied to eleven additional species, representing pathogenic, non-pathogenic and intermediate species and was demonstrated to rapidly differentiate all but 2 of the non-pathogenic Leptospira species. The method was applied successfully to infected tissues from field samples proving its value for diagnosing leptospiral infections found in animals in the UK. Crown Copyright (C) 2010 Published by Elsevier Ltd. All rights reserved.

Retrieval of phytoplankton size from bio-optical measurements: theory and applications

The absorption coefficient of a substance distributed as discrete particles in suspension is less than that of the same material dissolved uniformly in a medium—a phenomenon commonly referred to as the flattening effect. The decrease in the absorption coefficient owing to flattening effect depends on the concentration of the absorbing pigment inside the particle, the specific absorption coefficient of the pigment within the particle, and on the diameter of the particle, if the particles are assumed to be spherical. For phytoplankton cells in the ocean, with diameters ranging from less than 1 µm to more than 100 µm, the flattening effect is variable, and sometimes pronounced, as has been well documented in the literature. Here, we demonstrate how the in vivo absorption coefficient of phytoplankton cells per unit concentration of its major pigment, chlorophyll a, can be used to determine the average cell size of the phytoplankton population. Sensitivity analyses are carried out to evaluate the errors in the estimated diameter owing to potential errors in the model assumptions. Cell sizes computed for field samples using the model are compared qualitatively with indirect estimates of size classes derived from high performance liquid chromatography data. Also, the results are compared quantitatively against measurements of cell size in laboratory cultures. The method developed is easy-to-apply as an operational tool for in situ observations, and has the potential for application to remote sensing of ocean colour data.

Evaluation of PCR to detect Theileria parva in field-collected tick and bovine samples in Tanzania

The ability of PCR to detect infections of Theileria parva, the cause of East Coast Fever, in field-collected tick and bovine samples from Tanzania was evaluated. PCR-detected infection prevalence was high (15/20, 75%) in unfed adult Rhipicephalus appendiculatus ticks that fed as nymphs on an acutely-infected calf, but low (22/836, 2.6%) in unfed adult R. appendiculatus collected from field sites in Tanzania. Tick infection prevalence was comparable to that in previous studies that used salivary gland staining to detect T parva infection in field-collected host-seeking ticks. Of 282 naturally-exposed zebu calves, seven had PCR-positive buffy coat samples prior to detection of Theileria spp. parasites in stained huffy coat cells or lymph node biopsies. Evidence of Theileria spp. infections was detected in stained smears of lymph node biopsies from 109 calves (38.6%) and huffy coat samples from 81 (28.7%), while huffy coat samples from 66 (23.4%) were PCR-positive for T parva. Implications of these findings for the sensitivity and specificity of the PCR are discussed. (C) 2003 Elsevier Science B.V. All rights reserved.

Biological and chemical assessment of zinc ageing in field soils

As zinc (Zn) is both an essential trace element and potential toxicant, the effects of Zn fixation in soil are of practical significance. Soil samples from four field sites amended with ZnSO4 were used to investigate ageing of soluble Zn under field conditions over a 2-year period. Lability of Zn measured using 65Zn radioisotope dilution showed a significant decrease over time and hence evidence of Zn fixation in three of the four soils. However, 0.01 M CaCl2 extractions and toxicity measurements using a genetically modified lux-marked bacterial biosensor did not indicate a decrease in soluble/bioavailable Zn over time. This was attributed to the strong regulatory effect of abiotic properties such as pH on these latter measurements. These results also showed that Zn ageing occurred immediately after Zn spiking, emphasising the need to incubate freshly spiked soils before ecotoxicity assessments. Ageing effects were detected in Zn-amended field soils using 65Zn isotopic dilution as a measure of lability, but not with either CaCl2 extractions or a lux-marked bacterial biosensor.

The use of FT-IR as a screening technique for organic residue analysis of archaeological samples

A range of archaeological samples have been examined using FT-IR spectroscopy. These include suspected coprolite samples from the Neolithic site of Catalhoyuk in Turkey, pottery samples from the Roman site of Silchester, UK and the Bronze Age site of Gatas, Spain and unidentified black residues on pottery sherds from the Roman sites of Springhead and Cambourne, UK. For coprolite samples the aim of FT-IR analysis is identification. Identification of coprolites in the field is based on their distinct orange colour; however, such visual identifications can often be misleading due to their similarity with deposits such as ochre and clay. For pottery the aim is to screen those samples that might contain high levels of organic residues which would be suitable for GC-MS analysis. The experiments have shown coprolites to have distinctive spectra, containing strong peaks from calcite, phosphate and quartz; the presence of phosphorus may be confirmed by SEM-EDX analysis. Pottery containing organic residues of plant and animal origin has also been shown to generally display strong phosphate peaks. FT-IR has distinguished between organic resin and non-organic compositions for the black residues, with differences also being seen between organic samples that have the same physical appearance. Further analysis by CC-MS has confirmed the identification of the coprolites through the presence of coprostanol and bile acids, and shows that the majority of organic pottery residues are either fatty acids or mono- or di-acylglycerols from foodstuffs, or triterpenoid resin compounds exposed to high temperatures. One suspected resin sample was shown to contain no organic residues. and it is seen that resin samples with similar physical appearances have different chemical compositions. FT-IR is proposed as a quick and cheap method of screening archaeological samples before subjecting them to the more expensive and time-consuming method of GC-MS. This will eliminate inorganic samples such as clays and ochre from CC-MS analysis, and will screen those samples which are most likely to have a high concentration of preserved organic residues. (C) 2008 Elsevier B.V. All rights reserved.

The potential of grass field margin management for enhancing beetle diversity in intensive livestock farms

1. Declining populations of UK grassland flora and fauna have been attributed to intensification of agricultural management practices, including changes in cutting, fertilizer, grazing and drainage regimes. We aimed to develop field margin management practices that could reverse declines in intensively managed grassland biodiversity that would have application in the UK and Europe. Here we focus on one aspect of grassland biodiversity, the beetles. 2. In four intensively managed livestock farms in south-west England, 10-m wide field margins in existing grasslands were managed to create seven treatments of increasing sward architectural complexity. This was achieved through combinations of inorganic (NPK) fertilizer, cattle grazing, and timing and height of cutting. To examine the potential influence of complexity on faunal diversity, beetles were identified to species level from suction samples taken between 2003 and 2005, and their assemblage structure was related to margin management, floral assemblages and sward architecture. 3. Beetle abundance, and species richness and evenness were influenced by margin management treatment and its interaction with year. Correlations with sward architecture and the percentage cover of dominant forbs and grasses were also found. Functional groups of the beetles showed different responses to the management treatments. In particular, higher proportional abundances of seed/flower-feeding guilds were found in treatments not receiving NPK fertilizer. 4. The assemblage structure was shown to respond to margin management treatments, sward architecture and the percentage cover of dominant forbs and grasses. The most extensively managed treatments were characterized by distinct successional trajectories from the control treatment. 5. Synthesis and applications. This study provides management options suitable for use within agri-environment schemes intended to improve faunal diversity associated with intensively managed lowland grasslands. Field margins receiving either no management or a single July silage cut were shown to support greater abundances and species richness of beetles, although subtler modifications of conventional management may also be beneficial, for example the absence of NPK fertilizer while maintaining grazing and silage cutting systems.

Detection of Chlamydia psittaci DNA in avian clinical samples by polymerase chain reaction

A polymerase chain reaction (PCR) assay was developed to detect Chlamydia psittaci DNA in faeces and tissue samples from avian species. Primers were designed to amplify a 264 bp product derived from part of the 5' non-translated region and part of the coding region of the ompA gene which encodes the major outer membrane protein. Amplified sequences were confirmed by Southern hybridization using an internal probe. The sensitivity of the combined assay was found to be between 60 to 600 fg of chlamydial DNA (approximately 6 to 60 genome copies). The specificity of the assay was confirmed since PCR product was not obtained from samples containing several serotypes of C. trachomatis, strains of C. pneumoniae, the type strain of C. pecorum, nor from samples containing microorganisms commonly found in the avian gut flora. In this study, 404 avian faeces and 141 avian tissue samples received by the Central Veterinary Laboratory over a 6 month period were analysed by PCR, antigen detection ELISA and where possible, cell culture isolation. PCR performed favourably compared with ELISA and cell culture, or with ELISA alone. The PCR assay was especially suited to the detection of C. psittaci DNA in avian faeces samples. The test was also useful when applied to tissue samples from small contact birds associated with a case of human psittacosis where ELISA results were negative and chlamydial isolation was a less favourable method due to the need for rapid diagnosis.