Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita

Plant-parasitic nematodes are major agricultural pests worldwide and novel approaches to control them are sorely needed. We report the draft genome sequence of the root-knot nematode Meloidogyne incognita, a biotrophic parasite of many crops, including tomato, cotton and coffee. Most of the assembled sequence of this asexually reproducing nematode, totaling 86 Mb, exists in pairs of homologous but divergent segments. This suggests that ancient allelic regions in M. incognita are evolving toward effective haploidy, permitting new mechanisms of adaptation. The number and diversity of plant cell wall-degrading enzymes in M. incognita is unprecedented in any animal for which a genome sequence is available, and may derive from multiple horizontal gene transfers from bacterial sources. Our results provide insights into the adaptations required by metazoans to successfully parasitize immunocompetent plants, and open the way for discovering new antiparasitic strategies.

Development of a high-throughput enzyme-linked immunosorbent assay for the routine detection of the carcinogen acrylamide in food, via rapid derivatisation pre-analysis

The spontaneous formation of the neurotoxic carcinogen acrylamide in a wide range of cooked foods has recently been discovered. These foods include bread and other bakery products, crisps, chips, breakfast cereals, and coffee. To date, the diminutive size of acrylamide (71.08Da) has prevented the development of screening immunoassays for this chemical. In this study, a polyclonal antibody capable of binding the carcinogen was produced by the synthesis of an immunogen comprising acrylamide derivatised with 3-mercaptobenzoic acid (3-MBA), and its conjugation to the carrier protein bovine thyroglobulin. Antiserum from the immunised rabbit was harvested and fully characterised. it displayed no binding affinity for acrylamide or 3-MBA but had a high affinity for 3-MBA-derivitised acrylamide. The antisera produced was utilised in the development of an ELISA based detection system for acrylamide. Spiked water samples were assayed for acrylamide content using a previously published extraction method validated for coffee, crispbread, potato, milk chocolate and potato crisp matrices. Extracted acrylamide was then subjected to a rapid 1-h derivatisation with 3-MBA, pre-analysis. The ELISA was shown to have a high specificity for acrylamide, with a limit of detection in water samples of 65.7 mu g kg(-1), i.e. potentially suitable for acrylamide detection in a wide range of food commodities. Future development of this assay will increase sensitivity further. This is the first report of an immunoassay capable of detecting the carcinogen, as its small size has necessitated current analytical detection via expensive, slower, physico-chemical techniques such as Gas or Liquid Chromatography coupled to Mass Spectrometry. (c) 2007 Elsevier B.V. All rights reserved.

The legacy of past manuring practices on soil contamination in remote rural areas

This paper demonstrates that there can be a legacy of contamination on former arable land in remote rural areas as a result of past manuring practices. In the first part of the study four farms abandoned in the late 19th to mid-20th century were investigated with samples collected from residual material in domestic hearths, the midden heaps, kailyards (walled garden for vegetables), infields (intensively managed arable land) and outfields (less intensively managed land for cropping or grazing). Consistent sequences in concentration values were found for such elements as Pb, Zn, Cu and P in the order hearth>midden>kailyard>infield>outfield. Such patterns can in part be explained in terms of atmospheric deposition on peat and turf which were subsequently burnt in hearths to result in enhanced elemental concentrations. The ash then was deposited in midden heaps and subsequently on kailyards or infields. In the second part, microanalytical results from St. Kilda are discussed. Enhanced loadings of Pb and Zn were found in the old arable land. The highest levels of Zn were found in small fragments of carbonised and humified material and bone fragments; in contrast Pb tended to be more uniformly distributed. Seabird waste was extensively applied to the arable land and some of the Zn may have accumulated in the soil by this pathway. The retention of Zn in bone is likely to have been very minor given the rarity of bone fragments as evident in thin sections (0.3%); this compares with 6.8% for black carbonised particles which are likely to provide the main storage sites for Zn.

A posteriori-derived dietary patterns and retinal vessel caliber in an elderly population

Purpose. To examine the association between a posteriori–derived dietary patterns (DP) and retinal vessel caliber in an elderly population.

Methods. This was a cross-sectional study of 288 elderly adults (>65 years) who participated in the European Eye study (EUREYE) Northern Irish cohort. DP were extracted using principal component analysis from completed food frequency questionnaires. Semi-automated computer grading was used to determine the mean retinal vessel diameters (central retinal arteriole equivalent [CRAE] and central retinal venule equivalent [CRVE]) from digitized visual field one images using a standard measurement protocol.

Results. Three major DP were identified in this population, which accounted for 21% of the total variance: a “healthy” pattern with high factor loadings for oily fish, fruits and vegetables, and olive oil; an “unhealthy” pattern with high factor loadings for red and processed meat, refined grains, eggs, butter, sugar and sweets; and a “snack and beverage” pattern with high factor loading for pizza, nuts, and coffee. Multivariable linear regression analysis indicated no significant association between major identified DP and mean CRAE or CRVE in all models.

Conclusions. This is the first study to investigate associations between a posteriori–derived DP and retinal vessel caliber. There was no evidence of a relationship between extracted DP and retinal vessel measurements in this population. However, it is possible that potentially important relationships exist between single nutrients or foods and vessel diameters that cannot be identified using a DP approach. Further studies to examine the role of dietary factors in the microcirculation are required.

The lateritic profile of Balkouin, Burkina Faso: geochemistry, mineralogy and genesis

This study reports on the geochemical and mineralogical characterization of a lateritic profile cropping out in the Balkouin area, Central Burkina Faso, aimed at obtaining a better understanding of the processes responsible for the formation of the laterite itself and the constraints to its development. The lateritic profile rests on a Paleoproterozoic basement mostly composed of granodioritic rocks related to the Eburnean magmatic cycle passing upwards to saprolite and consists of four main composite horizons (bottom to top): kaolinite and clay-rich horizons, mottled laterite and iron-rich duricrust. In order to achieve such a goal, a multi-disciplinary analytical approach was adopted, which includes inductively coupled plasma (ICP) atomic emission and mass spectrometries (ICP-AES and ICP-MS respectively), X-ray powder diffraction (XRPD), scanning electron microscopy with energy dispersive spectrometry (SEM-EDS) and micro-Raman spectroscopy.

The geochemical data, and particularly the immobile elements distribution and REE patterns, show that the Balkouin laterite is the product of an in situ lateritization process that involved a strong depletion of the more soluble elements (K, Mg, Ca, Na, Rb, Sr and Ba) and an enrichment in Fe; Si was also removed, particularly in the uppermost horizons. All along the profile the change in composition is coupled with important changes in mineralogy. In particular, the saprolite is characterized by occurrence of abundant albitic plagioclase, quartz and nontronite; kaolinite is apparently absent. The transition to the overlying lateritic profile marks the breakdown of plagioclase and nontronite, thus allowing kaolinite to become one of the major components upwards, together with goethite and quartz. The upper part of the profile is strongly enriched in hematite (+ kaolinite). Ti oxides (at least in part as anatase) and apatite are typical accessory phases, while free aluminum hydroxides are notably absent. Mass change calculations emphasize the extent of the mass loss, which exceeds 50 wt% (and often 70 wt%) for almost all horizons; only Fe was significantly concentrated in the residual system.

The geochemical and mineralogical features suggest that the lateritic profile is the product of a continuous process that gradually developed from the bedrock upwards, in agreement with the Schellmann classic genetic model. The laterite formation must have occurred at low pH (? 4.5) and high Eh (? 0.4) values, i.e., under acidic and oxidizing environments, which allowed strongly selective leaching conditions. The lack of gibbsite and bohemite is in agreement with the compositional data: the occurrence of quartz (± amorphous silica) all along the profile was an inhibiting factor for the formation of free aluminum hydroxides.

Preaggregated Ag Nanoparticles in Dry Swellable Gel Films for Off-the-Shelf Surface-Enhanced Raman Spectroscopy

Large, thin (50 mu m) dry polymer sheets containing numerous surface-enhanced Raman spectroscopy (SERS) active Ag nanopartide aggregates have been prepared by drying aqueous mixtures of hydroxyethylcelloulose (HEC) and preaggregated Ag colloid in 10 x 10 cm molds. In these dry films, the particle aggregates are protected from the environment during storage and are easy to handle; for example, they can be cut to size with scissors. When in use, the highly swellable HEC polymer allowed the films to rapidly absorb aqueous analyte solutions while simultaneously releasing the Ag nanoparticle aggregates to interact with the analyte and generate large SERS signals. Either the films could be immersed in the analyte solution or 5 mu L droplets were applied to the surface; in the latter method, the local swelling caused the active area to dome upward, but the swollen film remained physically robust and could be handled as required. Importantly, encapsulation and release did not significantly compromise the SERS performance of the colloid; the signals given by the swollen films were similar to the very high signals obtained from the parent citrate-reduced colloid and were an order of magnitude larger than a commercially available nanoparticle substrate. These "Poly-SERS" films retained 70% of their SERS activity after being stored for 1 year in air. The films were sufficiently homogeneous to give a standard deviation of 3.2% in the absolute signal levels obtained from a test analyte, primarily due to the films' ability to suppress "coffee ring" drying marks, which meant that quantitative analysis without an internal standard was possible. The majority of the work used aqueous thiophenol as the test analyte; however, preliminary studies showed that the Poly-SERS films could also be used with nonaqueous solvents and for a range of other analytes including theophylline, a therapeutic drug, at a concentration as low as 1.0 x 10(-5) mol dm(-3) (1.8 mg/dm(3)), well below the sensitivity required for theophylline monitoring where the target range is 10-20 mg/dm(3).

Collaborative Scholarship on the Margins: An Epistolary Network

This article explores collaborative scholarship on the margins of intellectual life in eighteenth-century England via a close examination of George Ballard's collected correspondence from women letter-writers. Ballard was both a man of trade and an antiquary, and his modest social status inhibited his freedom to move in scholarly circles. Ballard's only published book documented the lives and works of "learned ladies" of Britain from the fifteenth to the eighteenth centuries, and his female correspondents included the Anglo-Saxon scholar Elizabeth Elstob. His collected correspondence provides an insight into a network that operated outside of the major institutions of scholarship and far from the coffee houses of metropolitan life, but which supported its participants in their intellectual endeavours. By examining the collection materially, and by plotting the correspondents geographically, a more precise picture can be drawn of how women and lower-status men could engage in intellectual life from the peripheries of scholarly society. 

Dietary habits of patients undergoing methadone therapy

OBJECTIVE: This study was designed to record the dietary habits of patients undergoing methadone therapy.

BACKGROUND: Numerous studies report that patients undergoing methadone treatment present with high levels of oral disease, especially dental caries. A number of factors have been described to account for this: sugared methadone preparations, prolonged oral retention, associated xerostomia and poor diet.

METHODS: A cross-sectional descriptive study using survey methodology was conducted of patients attending a non-resident drug rehabilitation clinic. A self-completion questionnaire and diet diary were developed and distributed to 66 patients over an 8 week period.

RESULTS: Of the 66 questionnaires distributed, 52 were successfully completed giving a response rate of 79%. 6 patients declined to complete the questionnaire. The surveyed patient pool consisted of 32 females (62%) and 20 males (38%) with a mean age of 32 years. All the participants were taking a prescribed daily dose of methadone when questioned. 68% of respondents consumed convience foods or sugary snacks every day. Of those patients who drank tea or coffee daily, 84% added sugar and 54% added 3 teaspoons or more. The majority of patients (71%) consumed at least one glass of a fizzy soft drink daily. In addition, the majority of respondents indicated that they snacked regularly between meals and 24% stated that they often woke up during the night for a snack. Patients recorded their last intake of food ranging from 5pm to 3am.

CONCLUSIONS: The patients surveyed had poor dietary habits. Respondents consumed a large amount of convience foods and sugars during mealtimes and through regular snacking. Dietary counselling should be considered as part of treatment for patients undergoing methadone therapy.

Swift and Conversational Culture

Swift often noted his aversion to coffee-house conversation and to tavern talk, to gossip and company, and to being buried in Dublin in the years of his Deanship. Yet the popular myth of a morose, unsociable Swift belies both his engagement with various literary and political clubs in his early career and his participation in collaborative and experimental poetic games in his Dublin circles. This essay considers Swift’s involvement with three clubs in London (the Saturday Club, the Brothers’ Club, and the Scriblerians) and his writings on a number of fictional clubs (the Athenian Society, the Calves-Head Club, and a putative Society for the correction of the English language). While Swift wrote very little of his experience of actual clubs, the latter three, in addition to the Scriblerian Club as an imagined, rather than actual clubs, resulted in a number of defining poems and works in his career. When Swift settled in Dublin, poetry written and exchanged in a number of sociable circles characterised much of his published verse and gave glimpses of the circles and informal clubs which he formed among friends there. Although these poems are often dismissed as ‘trifles’, the essay argues that the poems are crucial for our understandings of ‘conversational culture’ or sociability in Swift’s Dublin.

Rethinking Rice Preparation for Highly Efficient Removal of Inorganic Arsenic Using Percolating Cooking Water

A novel way of cooking rice to maximize the removal of the carcinogen inorganic arsenic (Asi) is presented here. In conventional rice cooking water and grain are in continuous contact, and it is known that the larger the water:rice cooking ratio, the more Asi removed by cooking, suggesting that the Asi in the grain is mobile in water. Experiments were designed where rice is cooked in a continual stream of percolating near boiling water, either low in Asi, or Asi free. This has the advantage of not only exposing grain to large volumes of cooking water, but also physically removes any Asi leached from the grain into the water receiving vessel. The relationship between cooking water volume and Asi removal in conventional rice cooking was demonstrated for the rice types under study. At a water-to-rice cooking ratio of 12:1, 57±5% of Asi could be removed, average of 6 wholegrain and 6 polished rice samples. Two types of percolating technology were tested, one where the cooking water was recycled through condensing boiling water steam and passing the freshly distilled hot water through the grain in a laboratory setting, and one where tap water was used to cook the rice held in an off-the-shelf coffee percolator in a domestic setting. Both approaches proved highly effective in removing Asi from the cooking rice, with up to 85% of Asi removed from individual rice types. For the recycled water experiment 59±8% and 69±10% of Asi was removed, on average, compared to uncooked rice for polished (n=27) and wholegrain (n=13) rice, respectively. For coffee percolation there was no difference between wholegrain and polished rice, and the effectiveness of Asi removal was 49±7% across 6 wholegrain and 6 polished rice samples. The manuscript explores the potential applications and further optimization of this percolating cooking water, high Asi removal, discovery.

MESAS

MESAS is an urban intervention that promotes the relationship with everyday sound through indispensable pieces of furniture for the domestic, the professional and the playful in our lives – the table. Different uses and contexts determine the many variations in form; from dinning, to coffee tables, kitchen, garden, meeting, bar, side or game tables. The MESAS project, by artists Pedro Rebelo and Ricardo Jacinto was conceived for Rua Direita in Viseu and consists of a sequence of tables suspended throughout the street, which reveal experiences and memories through sound. The materiality, context and utility of each table articulate sonorities that include the manipulation of objects on their tops or the conversations happening around them, as well their impact on the soundscapes of the places in which they are situated. The project makes audible these particular experiences through a set of sound installations associated with places such as the jewellery, the school, or the tailor’s.