A novel method for the transport and analysis of genetic material from polyps and zooxanthellae of scleractinian corals

We have developed a new simple method for transport, storage, and analysis of genetic material from the corals Agaricia agaricites, Dendrogyra cylindrica, Eusmilia ancora, Meandrina meandrites, Montastrea annularis, Porites astreoides, Porites furcata, Porites porites, and Siderastrea siderea at room temperature. All species yielded sufficient DNA from a single FTA(R) card (19 mug-43 ng) for subsequent PCR amplification of both coral and zooxanthellar DNA. The D1 and D2 variable region of the large Subunit rRNA gene (LSUrDNA) was amplified from the DNA of P. furcata and S. siderea by PCR. Electrophoresis yielded two major DNA bands: an 800-base pair (bp) DNA, which represented the coral ribosomal RNA (rRNA) gene, and a 600-bp DNA, which represented the zooxanthellar srRNA gene. Extraction of DNA from the bands yielded between 290 mug total DNA (S. siderea coral DNA) and 9 mug total DNA (P. furcata zooxanthellar DNA). The ability to transport and store genetic material from scleractinian corals without resort to laboratory facilities in the field allows for the molecular Study of a far wider range and variety of coral sites than have been studied to date. (C) 2003 Elsevier Science B.V. All rights reserved.

A new method for the characterisation and verification of local spatial predictability for convective scale ensembles

The use of kilometre-scale ensembles in operational forecasting provides new challenges for forecast interpretation and evaluation to account for uncertainty on the convective scale. A new neighbourhood based method is presented for evaluating and characterising the local predictability variations from convective scale ensembles. Spatial scales over which ensemble forecasts agree (agreement scales, S^A) are calculated at each grid point ij, providing a map of the spatial agreement between forecasts. By comparing the average agreement scale obtained from ensemble member pairs (S^A(mm)_ij), with that between members and radar observations (S^A(mo)_ij), this approach allows the location-dependent spatial spread-skill relationship of the ensemble to be assessed. The properties of the agreement scales are demonstrated using an idealised experiment. To demonstrate the methods in an operational context the S^A(mm)_ij and S^A(mo)_ij are calculated for six convective cases run with the Met Office UK Ensemble Prediction System. The S^A(mm)_ij highlight predictability differences between cases, which can be linked to physical processes. Maps of S^A(mm)_ij are found to summarise the spatial predictability in a compact and physically meaningful manner that is useful for forecasting and for model interpretation. Comparison of S^A(mm)_ij and S^A(mo)_ij demonstrates the case-by-case and temporal variability of the spatial spread-skill, which can again be linked to physical processes.

A simple method of calculating eigenvalues and resonances in domains with infinite regular ends

A new approach is presented for the solution of spectral problems on infinite domains with regular ends, which avoids the need to solve boundary-value problems for many trial values of the spectral parameter. We present numerical results both for eigenvalues and for resonances, comparing with results reported by Aslanyan, Parnovski and Vassiliev.

Comparing sampling needs for variograms of soil properties computed by the method of moments and residual maximum likelihood

It has been generally accepted that the method of moments (MoM) variogram, which has been widely applied in soil science, requires about 100 sites at an appropriate interval apart to describe the variation adequately. This sample size is often larger than can be afforded for soil surveys of agricultural fields or contaminated sites. Furthermore, it might be a much larger sample size than is needed where the scale of variation is large. A possible alternative in such situations is the residual maximum likelihood (REML) variogram because fewer data appear to be required. The REML method is parametric and is considered reliable where there is trend in the data because it is based on generalized increments that filter trend out and only the covariance parameters are estimated. Previous research has suggested that fewer data are needed to compute a reliable variogram using a maximum likelihood approach such as REML, however, the results can vary according to the nature of the spatial variation. There remain issues to examine: how many fewer data can be used, how should the sampling sites be distributed over the site of interest, and how do different degrees of spatial variation affect the data requirements? The soil of four field sites of different size, physiography, parent material and soil type was sampled intensively, and MoM and REML variograms were calculated for clay content. The data were then sub-sampled to give different sample sizes and distributions of sites and the variograms were computed again. The model parameters for the sets of variograms for each site were used for cross-validation. Predictions based on REML variograms were generally more accurate than those from MoM variograms with fewer than 100 sampling sites. A sample size of around 50 sites at an appropriate distance apart, possibly determined from variograms of ancillary data, appears adequate to compute REML variograms for kriging soil properties for precision agriculture and contaminated sites. (C) 2007 Elsevier B.V. All rights reserved.

Development of a capillary electrophoresis method for the simultaneous analysis of artificial sweeteners, preservatives and colours in soft drinks

A rapid capillary electrophoresis method was developed simultaneously to determine artificial sweeteners, preservatives and colours used as additives in carbonated soft drinks. Resolution between all additives occurring together in soft drinks was successfully achieved within a 15-min run-time by employing the micellar electrokinetic chromatography mode with a 20 mM carbonate buffer at pH 9.5 as the aqueous phase and 62 mM sodium dodecyl sulfate as the micellar phase. By using a diode-array detector to monitor the UV-visible range (190-600 nm), the identity of sample components, suggested by migration time, could be confirmed by spectral matching relative to standards.

Drying method influences the development of germinability, dessication tolerance and subsequent longevity of immature seeds of sumauma (Ceiba pentandra (L.) Gaertn. [Bombacaceae])

The ability to germinate, tolerate desiccation and survive in air-dry storage was investigated during early seed development in planta and subsequent ex planta maturation of sumauma (Ceiba pentandra). Immature fruits were collected on three different dates (i.e. from about 5 days before until 7 days after mass maturity). Immature fresh seeds were not able to germinate. Fruits or seeds were subjected immediately after each collection to three different drying treatments with progressively slower rates of dessication: (i) seeds were extracted from the fruits and dried immediately; (ii) fruits were dried in a thin layer; (iii) fruits were dried in a tied polyethylene bag (with 10 holes of 1cm diameter). Drying was in a room maintained at 25 degrees C +/- 3 degrees C and 65%+/- 5% r.h. For treatment (i) the seeds were dried for 6 days in order to reduce moisture content to around 13% ( +/- 2%) moisture content. For treatments (ii) and (iii) the fruits were subjected to different periods of drying depending upon collection date. The results of these post-collection treatments showed generally that the more immature the seeds the slower the rate of drying that is required to improve ability to germinate, ability to tolerate desiccation and potential longevity, but at the third harvest, 7 days after mass maturity, the intermediate drying rate treatment was the most beneficial. Thus post fruit collection treatments can be modified depending upon the stage of seed development in order to provide good to high quality seeds of sumauma when collection has to be made at a site with difficult access at less than ideal times. The results are relevant to seed collection practices for both forestry and ex situ plant biodiversity conservation.

The tagged microarray marker (TAM) method for high-throughput detection of single nucleotide and indel polymorphisms

The tagged microarray marker (TAM) method allows high-throughput differentiation between predicted alternative PCR products. Typically, the method is used as a molecular marker approach to determining the allelic states of single nucleotide polymorphisms (SNPs) or insertion-deletion (indel) alleles at genomic loci in multiple individuals. Biotin-labeled PCR products are spotted, unpurified, onto a streptavidin-coated glass slide and the alternative products are differentiated by hybridization to fluorescent detector oligonucleotides that recognize corresponding allele-specific tags on the PCR primers. The main attractions of this method are its high throughput (thousands of PCRs are analyzed per slide), flexibility of scoring (any combination, from a single marker in thousands of samples to thousands of markers in a single sample, can be analyzed) and flexibility of scale (any experimental scale, from a small lab setting up to a large project). This protocol describes an experiment involving 3,072 PCRs scored on a slide. The whole process from the start of PCR setup to receiving the data spreadsheet takes 2 d.

Development of a liquid chromatographic time-of-flight mass spectrometric method for the determination of unlabelled and deuterium-labelled alpha-tocopherol in blood components

A method is described for the analysis of deuterated and undeuterated alpha-tocopherol in blood components using liquid chromatography coupled to an orthogonal acceleration time-of-flight (TOF) mass spectrometer. Optimal ionisation conditions for undeuterated (d0) and tri- and hexadeuterated (d3 or d6) alpha-tocopherol standards were found with negative ion mode electrospray ionisation. Each species produced an isotopically resolved single ion of exact mass. Calibration curves of pure standards were linear in the range tested (0-1.5 muM, 0-15 pmol injected). For quantification of d0 and d6 in blood components following a standard solvent extraction, a stable-isotope-labelled internal standard (d3-alpha-tocopherol) was employed. To counter matrix ion suppression effects, standard response curves were generated following identical solvent extraction procedures to those of the samples. Within-day and between-day precision were determined for quantification of d0- and d6-labelled alpha-tocopherol in each blood component and both averaged 3-10%. Accuracy was assessed by comparison with a standard high-performance liquid chromatography (HPLC) method, achieving good correlation (r(2) = 0.94), and by spiking with known concentrations of alpha-tocopherol (98% accuracy). Limits of detection and quantification were determined to be 5 and 50 fmol injected, respectively. The assay was used to measure the appearance and disappearance of deuterium-labelled alpha-tocopherol in human blood components following deuterium-labelled (d6) RRR-alpha-tocopheryl acetate ingestion. The new LC/TOFMS method was found to be sensitive, required small sample volumes, was reproducible and robust, and was capable of high throughput when large numbers of samples were generated. Copyright (C) 2003 John Wiley Sons, Ltd.

Mild and rapid method for the generation of ortho-(naphtho)-quinone methide intermediates

A new mild method has been devised for generating o-(naphtho)quinone methides via fluoride-induced desilylation of silyl derivatives of o-hydroxybenzyl(or 1-naphthylmethyl) nitrate. The reactive o-(naphtho)quinone methide intermediates were trapped by C, O, N and S nucleophiles and underwent “inverse electron-demand” hetero Diels- Alder reaction with dienophiles to give stable adducts. The method has useful potential application in natural product synthesis and drug research

A simplified method for referring the energy and overheating performance of window design

This paper describes a simplified dynamic thermal model which simulates the energy and overheating performance of windows. To calculate artificial energy use within a room, the model employs the average illuminance method, which takes into account the daylight energy impacting upon the room by the use of hourly climate data. This tool describes the main thermal performance ( heating, cooling and overheating risk) resulting proposed a design of window. The inputs are fewer and simpler than that are required by complicated simulation programmes. The method is suited for the use of architects and engineers at the strategic phase of design, when little is available.

Development and application of a method for the purification of free shigatoxigenic bacteriophage from environmental samples

Shiga toxin producing Escherichia coli (STEC) strains are foodborne pathogens whose ability to produce Shiga toxin (Stx) is due to the integration of Stx-encoding lambdoid bacteriophage (Stx phage). Circulating, infective Stx phages are very difficult to isolate, purify and propagate such that there is no information on their genetic composition and properties. Here we describe a novel approach that exploits the phage's ability to infect their host and form a lysogen, thus enabling purification of Stx phages by a series of sequential lysogen isolation and induction steps. A total of 15 Stx phages were rigorously purified from water samples in this way, classified by TEM and genotyped using a PCR-based multi-loci characterisation system. Each phage possessed only one variant of each target gene type, thus confirming its purity, with 9 of the 15 phages possessing a short tail-spike gene and identified by TEM as Podoviridae. The remaining 6 phages possessed long tails, four of which appeared to be contractile in nature (Myoviridae) and two of which were morphologically very similar to bacteriophage lambda (Siphoviridae).

Harringtonian virtue: Harrington, Machiavelli, and the method of the 'Moment'

This article presents a reinterpretation of James Harrington's writings. It takes issue with J. G. A. Pocock's reading, which treats him as importing into England a Machiavellian ‘language of political thought’. This reading is the basis of Pocock's stress on the republicanism of eighteenth-century opposition values. Harrington's writings were in fact a most implausible channel for such ideas. His outlook owed much to Stoicism. Unlike the Florentine, he admired the contemplative life; was sympathetic to commerce; and was relaxed about the threat of ‘corruption’ (a concept that he did not understand). These views can be associated with his apparent aims: the preservation of a national church with a salaried but politically impotent clergy; and the restoration of the royalist gentry to a leading role in English politics. Pocock's hypothesis is shown to be conditioned by his method; its weaknesses reflect some difficulties inherent in the notion of ‘languages of thought’.

On the stability and convergence of the finite section method for integral equation formulations of rough surface scattering

We consider the Dirichlet and Robin boundary value problems for the Helmholtz equation in a non-locally perturbed half-plane, modelling time harmonic acoustic scattering of an incident field by, respectively, sound-soft and impedance infinite rough surfaces.Recently proposed novel boundary integral equation formulations of these problems are discussed. It is usual in practical computations to truncate the infinite rough surface, solving a boundary integral equation on a finite section of the boundary, of length 2A, say. In the case of surfaces of small amplitude and slope we prove the stability and convergence as A→∞ of this approximation procedure. For surfaces of arbitrarily large amplitude and/or surface slope we prove stability and convergence of a modified finite section procedure in which the truncated boundary is ‘flattened’ in finite neighbourhoods of its two endpoints. Copyright © 2001 John Wiley & Sons, Ltd.