Effect of habitat fragmentation on levels and patterns of genetic diversity in natural populations of the peat moss Polytrichum commune

Peat bogs represent unique ecosystems that are under particular threat from fragmentation due to peat harvesting, with only 38% of the original peatland in Europe remaining intact and unaffected by peat cutting, drainage and silviculture. In this study, we have used microsatellite markers to determine levels and patterns of genetic diversity in both cut and uncut natural populations of the peat moss Polytrichum commune. Overall diversity levels suggest that there is more genetic variation present than had previously been assumed for bryophytes. Despite this, diversity values from completely cut bogs were found to be lower than those from uncut peatlands (average 0.729 versus 0.880). In addition, the genetic diversity was more highly structured in the cut populations, further suggesting that genetic drift is already affecting genetic diversity in peat bogs subjected to fragmentation.

Development of microsatellites for the peat moss Sphagnum capillifolium using ISSR cloning

Sphagnum mosses are major components of peat bogs but populations of many species are under threat due to habitat fragmentation resulting from the cutting of peat for fuel. We have used an intersimple sequence repeat (ISSR)-based cloning method to develop nine polymorphic nuclear microsatellites for the peat moss species Sphagnum capillifolium. Between three and seven alleles per locus were detected in a sample of 48 haploid gametophytes and levels of gene diversity ranged from 0.5391 to 0.7960. These represent the first microsatellite markers developed for this important genus and most also exhibited cross-species amplification across a range of common Sphagnum species.

Adsorption characteristics of Cu and Ni on Irish peat moss

Peat has been widely used as a low cost adsorbent to remove a variety of materials including organic compounds and heavy metals from water. Various functional groups in lignin allow such compounds to bind on active sites of peat. The adsorption of Cu²⁺ and Ni²⁺ from aqueous solutions on Irish peat moss was studied both as a pure ion and from their binary mixtures under both equilibrium and dynamic conditions in the concentration range of 5–100 mg/L. The pH of the solutions containing either Cu²⁺ or Ni²⁺ was varied over a range of 2–8. The adsorption of Cu²⁺ and Ni⁺² on peat was found to be pH dependent. The adsorption data could be fitted to a two-site Langmuir adsorption isotherm and the maximum adsorption capacity of peat was determined to be 17.6 mg/g for Cu²⁺ and 14.5 mg/g for Ni²⁺ at 298 K when the initial concentration for both Cu²⁺ and Ni²⁺ was 100 mg/L, and the pH of the solution was 4.0 and 4.5, respectively. Column studies were conducted to generate breakthrough data for both pure component and binary mixtures of copper and nickel. Desorption experiments showed that 2 mM EDTA solution could be used to remove all of the adsorbed copper and nickel from the bed.

Efficacy of sod removal in regenerating fen vegetation for the conservation of the marsh fritillary butterfly Euphydryas aurinia, Montiaghs Moss Nature Reserve, County Antrim, Northern Ireland.

The efficacy of ‘sod removal’ as a fenland restoration technique was tested using an experimental approach at Montiaghs Moss Nature Reserve, Northern Ireland, from 2006 to 2008. The site suffered from rank growth of purple moor-grass Molinia caerulea which was out-competing herbaceous species. Soil was removed up to a depth of 15 cm completely denuding vegetation in the experimental plot exposing bare peat. By July 2007, 15.2% of sod-removal areas were revegetated; by October 2008 cover had risen to 64.6%. Of this cover, purple moor-grass accounted for only 9-11% compared to 78- 79% on control plots. Cover of other rank-forming grass species was also significantly reduced. Sod removal significantly increased the cover of species characteristic of fenlands including sedges Carex spp., rushes Juncus spp., marsh pennywort Hydrocotyle vulgaris and lesser spearwort Ranunculus flammula. It seems likely that sod removal, which lowered the surface of the peat, restored minerotrophic conditions and exposed the historical seed bank stimulating regeneration of some fenland specialists and pioneer species; this resulted in significantly higher species richness on sod removal plots than control plots two years after treatment. There was no demonstrable effect of sod removal on abundance of devil’s-bit scabious Succisa pratensis, the larval food plant of the Annex II listed marsh fritillary butterfly Euphydryas aurinia. We recommend that consideration should be given to artificially seeding devil’s-bit scabious soon after sod removal treatment to promote early recolonisation and to increase plant abundance on the site.

Analogies between linguistics and information theory

An analogy is established between the syntagm and paradigm from Saussurean linguistics and the message and messages for selection from the information theory initiated by Claude Shannon. The analogy is pursued both as an end itself and for its analytic value in understanding patterns of retrieval from full text systems. The multivalency of individual words when isolated from their syntagm is contrasted with the relative stability of meaning of multi-word sequences, when searching ordinary written discourse. The syntagm is understood as the linear sequence of oral and written language. Saussureâ??s understanding of the word, as a unit which compels recognition by the mind, is endorsed, although not regarded as final. The lesser multivalency of multi-word sequences is understood as the greater determination of signification by the extended syntagm. The paradigm is primarily understood as the network of associations a word acquires when considered apart from the syntagm. The restriction of information theory to expression or signals, and its focus on the combinatorial aspects of the message, is sustained. The message in the model of communication in information theory can include sequences of written language. Shannonâ??s understanding of the written word, as a cohesive group of letters, with strong internal statistical influences, is added to the Saussurean conception. Sequences of more than one word are regarded as weakly correlated concatenations of cohesive units.

Cybr, a cytokine-inducible protein that binds cytohesin-1 and regulates its activity

Cytokines regulate lymphocyte development and differentiation, but precisely how they control these processes is still poorly understood. By using microarray technology to detect cytokine-induced genes, we identified a cDNA encoding Cybr, which was increased markedly in cells incubated with IL-2 and IL-12. The mRNA was most abundant in hematopoietic cells and tissues. The predicted amino acid sequence is similar to that of GRP-1-associated protein (GRASP), a recently identified retinoic acid-induced cytohesin-binding protein. Physical interaction, dependent on the coiled-coil domains of Cybr and cytohesin-1, was demonstrated by coimmunoprecipitation of the overexpressed proteins from 293T cells. Cytohesin-1, in addition to its role in cell adhesion, is a guanine nucleotide-exchange protein activator of ARF GTPases. Acceleration of guanosine 5'-O-(thiotriphosphate) binding to ARF by cytohesin-1 in vitro was enhanced by Cybr. Because the binding protein modified activation of ADP ribosylation factor by cytohesin-1, we designate this cytokine-inducible protein Cybr (cytohesin binder and regulator).

Load Testing of Floor Slabs in a Full-Scale Reinforced Concrete Building

A series of short and long term service load tests were undertaken on the sixth floor of the full-scale, seven storey, reinforced concrete building at the Large Building Test Facility of the Building Research Establishment at Cardington. By using internally strain gauged reinforcing bars cast into an internal and external floor bay during the construction process it was possible to gain a detailed record of slab strains resulting from the application of several arrangements of test loads. Short term tests were conducted in December 1998 and long term monitoring then ensued until April 2001. This paper describes the test programmes and presents results to indicate slab behaviour for the various loading regimes.

Prediction of adipose tissue composition using Raman spectroscopy: average properties and individual fatty acids.

Abstract: Raman spectroscopy has been used for the first time to predict the FA composition of unextracted adipose tissue of pork, beef, lamb, and chicken. It was found that the bulk unsaturation parameters could be predicted successfully [R-2 = 0.97, root mean square error of prediction (RMSEP) = 4.6% of 4 sigma], with cis unsaturation, which accounted for the majority of the unsaturation, giving similar correlations. The combined abundance of all measured PUFA (>= 2 double bonds per chain) was also well predicted with R-2 = 0.97 and RMSEP = 4.0% of 4 sigma. Trans unsaturation was not as well modeled (R-2 = 0.52, RMSEP = 18% of 4 sigma); this reduced prediction ability can be attributed to the low levels of trans FA found in adipose tissue (0.035 times the cis unsaturation level). For the individual FA, the average partial least squares (PLS) regression coefficient of the 18 most abundant FA (relative abundances ranging from 0.1 to 38.6% of the total FA content) was R-2 = 0.73; the average RMSEP = 11.9% of 4 sigma. Regression coefficients and prediction errors for the five most abundant FA were all better than the average value (in some cases as low as RMSEP = 4.7% of 4 sigma). Cross-correlation between the abundances of the minor FA and more abundant acids could be determined by principal component analysis methods, and the resulting groups of correlated compounds were also well-predicted using PLS. The accuracy of the prediction of individual FA was at least as good as other spectroscopic methods, and the extremely straightforward sampling method meant that very rapid analysis of samples at ambient temperature was easily achieved. This work shows that Raman profiling of hundreds of samples per day is easily achievable with an automated sampling system.

A critical evaluation of Raman spectroscopy for the analysis of lipids: fatty acid methyl esters.

The work presented here is aimed at determining the potential and limitations of Raman spectroscopy for fat analysis by carrying out a systematic investigation of C-4-C-24 FAME. These provide a simple, well-characterized set of compounds in which the effect of making incremental changes can be studied over a wide range of chain lengths and degrees of unsaturation. The effect of temperature on the spectra was investigated over much larger ranges than would normally be encountered in real analytical measurements. It was found that for liquid FAME the best internal standard band was the carbonyl stretching vibration nu(C = O), whose position is affected by changes in sample chain length and physical state; in the samples studied here, it was found to lie between 1729 and 1748 cm(-1). Further, molar unsaturation could be correlated with the ratio of the nu(C = O) to either nu(C = C) or delta(H-C = ) with R-2 > 0.995. Chain length was correlated with the delta(CH2)(tw)/nu(C = O) ratio, (where "tw" indicates twisting) but separate plots for odd- and even-numbered carbon chains were necessary to obtain R-2 > 0.99 for liquid samples. Combining the odd- ani even-numbered carbon chain data in a single plot reduced the correlation to R-2 = 0.94-0.96, depending on the band ratios used. For molal unsaturation the band ratio that correlated linearly with unsaturation (R-2 > 0.99) was nu(C = C)/delta(CH2)(SC) (where "sc" indicates scissoring). Other band ratios show much more complex behavior with changes in chemical and physical structure. This complex behavior results from the fact that the bands do not arise from simple vibrations of small, discrete regions of the molecules but are due to complex motions of large sections of the FAME so that making incremental changes in structure does not necessarily lead to simple incremental changes in spectra.

Multivariate prediction of clarified butter composition using Raman spectroscopy

Raman spectroscopy has been used to predict the abundance of the FA in clarified butterfat that was obtained from dairy cows fed a range of levels of rapeseed oil in their diet. Partial least squares regression of the Raman spectra against FA compositions obtained by GC showed good prediction for the five major (abundance >5%) FA with R-2=0.74-0.92 and a root mean SE of prediction (RMSEP) that was 5-7% of the mean. In general, the prediction accuracy fell with decreasing abundance in the sample, but the RMSEP was 1.25%. The Raman method has the best prediction ability for unsaturated FA (R-2=0.85-0.92), and in particular trans unsaturated FA (best-predicted FA was 18:1 tDelta9). This enhancement was attributed to the isolation of the unsaturated modes from the saturated modes and the significantly higher spectral response of unsaturated bonds compared with saturated bonds. Raman spectra of the melted butter samples could also be used to predict bulk parameters calculated from standard analyzes, such as iodine value (R-2=0.80) and solid fat content at low temperature (R-2=0.87). For solid fat contents determined at higher temperatures, the prediction ability was significantly reduced (R-2=0.42), and this decrease in performance was attributed to the smaller range of values in solid fat content at the higher temperatures. Finally, although the prediction errors for the abundances of each of the FA in a given sample are much larger with Raman than with full GC analysis, the accuracy is acceptably high for quality control applications. This, combined with the fact that Raman spectra can be obtained with no sample preparation and with 60-s data collection times, means that high-throughput, on-line Raman analysis of butter samples should be possible.

DFT studies of long-chain FAMEs: theoretical justification for determining chain length and unsaturation from experimental Raman spectra

Density functional calculations, using B3LPY/6-31G(d) methods, have been used to investigate the conformations and vibrational (Raman) spectra of a series of long-chain, saturated fatty acid methyl esters (FAMEs) with the formula CH2nO2 (n = 5-21) and two series of unsaturated FAMEs. The calculations showed that the lowest energy conformer within the saturated FAMEs is the simple (all-trans) structure and, in general, it was possible to reproduce experimental data using calculations on only the all-trans conformer. The only exception was C6H12O2, where a second low-lying conformer had to be included in order to correctly simulate the experimental Raman spectrum. The objective of the work was to provide theoretical justification for the methods that are commonly used to determine the properties of the fats and oils, such as chain length and degree of unsaturation, from experimental Raman data. Here it is shown that the calculations reproduce the trends and calibration curves that are found experimentally and also allow the reasons for the failure of what would appear to be rational measurements to be understood. This work shows that although the assumption that each FAME can simply be treated as a collection of functional groups can be justified in some cases, many of the vibrational modes are complex motions of large sections of the molecules and thus would not be expected to show simple linear trends with changes in structure, such as increasing chain length and/or unsaturation. Simple linear trends obtained from experimental data may thus arise from cancellation of opposing effects, rather than reflecting an underlying simplicity.

Conformations, vibrational frequencies and Raman intensities of short-chain fatty acid methyl esters using DFT with 6-31G(d) and Sadlej pVTZ basis sets

Density functional calculations, using B3LPY/6-31G(d) methods, have been used to investigate the conformations and vibrational (Raman) spectra of three short-chain fatty acid methyl esters (FAMEs) with the formula CnH2nO2 (n = 3-5). In all three FAMEs, the lowest energy conformer has a simple 'all-trans' structure but there are other conformers, with different torsions about the backbone, which lie reasonably close in energy to the global minimum. One result of this is that the solid samples we studied do not appear to consist entirely of the lowest energy conformer. Indeed, to account for the 'extra' bands that were observed in the Raman data but were not predicted for the all-trans conformer, it was necessary to add-in contributions from other conformers before a complete set of vibrational assignments could be made. Provided this was done, the agreement between experimental Raman frequencies and 6-31G(d) values (after scaling) was excellent, RSD = 12.6 cm(-1). However, the agreement between predicted and observed intensities was much less satisfactory. To confirm the validity of the approach followed by the 6-3 1 G(d) basis set, we used a larger basis set, Sadlej pVTZ, and found that these calculations gave accurate Raman intensities and simulated spectra (summed from two different conformers) that were in quantitative agreement with experiment. In addition, the unscaled Sadlej pVTZ, and the scaled 6-3 1 G(d) calculations gave the same vibrational mode assignments for all bands in the experimental data. This work provides the foundation for calculations on longer-chain FAMEs (which are closer to those found as triglycerides in edible fats and oils) because it shows that scaled 6-3 1 G(d) calculations give equally accurate frequency predictions, and the same vibrational mode assignments, as the much more CPU-expensive Sadlej pVTZ basis set calculations.

Preliminary investigation of the application of Raman spectroscopy to the prediction of the sensory quality of beef silverside

The potential of Raman spectroscopy for the determination of meat quality attributes has been investigated using data from a set of 52 cooked beef samples, which were rated by trained taste panels. The Raman spectra, shear force and cooking loss were measured and PLS used to correlate the attributes with the Raman data. Good correlations and standard errors of prediction were found when the Raman data were used to predict the panels' rating of acceptability of texture (R-2 = 0.71, Residual Mean Standard Error of Prediction (RMSEP)% of the mean (mu) = 15%), degree of tenderness (R-2 = 0.65, RMSEP% of mu = 18%), degree of juiciness (R-2 = 0.62, RMSEP% of mu = 16%), and overall acceptability (R-2 = 0.67, RMSEP% of mu = 11%). In contrast, the mechanically determined shear force was poorly correlated with tenderness (R-2 = 0.15). Tentative interpretation of the plots of the regression coefficients suggests that the alpha-helix to beta-sheet ratio of the proteins and the hydrophobicity of the myofibrillar environment are important factors contributing to the shear force, tenderness, texture and overall acceptability of the beef. In summary, this work demonstrates that Raman spectroscopy can be used to predict consumer-perceived beef quality. In part, this overall success is due to the fact that the Raman method predicts texture and tenderness, which are the predominant factors in determining overall acceptability in the Western world. Nonetheless, it is clear that Raman spectroscopy has considerable potential as a method for non-destructive and rapid determination of beef quality parameters.