Impact of sewage sludge applications on the biogeochemistry of soils

This report describes an investigation into the bioavailability and fate of trace metals and their subsequent impact on important soil microbiological functions such as nitrification, denitrification and methane oxidation in low and high Cu containing soils in the presence and absence of residual organic matter from sewage sludge additions made 10 years earlier. The soils being studied are part of long term sewage sludge trials and include a low Cu soil ( 13.3mg Cu/ kg soil, 4.18 LOI %), left un- amended to serve as a control soil, soil amended with a high Cu sewage sludge ( 278.3mg Cu/ kg soil, 6.52 LOI %) and soil amended with a low Cu sewage sludge ( 46.3mg Cu/ kg soil, 6.18 LOI %). Soil was also amended with inorganic metal salts ( 273.4mg Cu/ kg soil, 4.52 LOI %) to further investigate the impact of Cu in the absence of additional organic matter contained in applied sewage sludge. Data from the first two years of a project are presented which has included field- based studies at long term sewage sludge trials based in Watlington, Oxford, UK and laboratory based studies at the Institute of Grassland & Environmental Research, North Wyke, Devon, UK.

Tin and mercury

This chapter contains sections titled: Introduction Geogenic Occurrence Sources of Soil Contamination Chemical Behaviour in Soils Risks from Tin and Mercury in Soils References

In-street wind direction variability in the vicinity of a busy intersection in central London

We present results from fast-response wind measurements within and above a busy intersection between two street canyons (Marylebone Road and Gloucester Place) in Westminster, London taken as part of the DAPPLE (Dispersion of Air Pollution and Penetration into the Local Environment; www.dapple.org.uk) 2007 field campaign. The data reported here were collected using ultrasonic anemometers on the roof-top of a building adjacent to the intersection and at two heights on a pair of lamp-posts on opposite sides of the intersection. Site characteristics, data analysis and the variation of intersection flow with the above-roof wind direction (θref) are discussed. Evidence of both flow channelling and recirculation was identified within the canyon, only a few metres from the intersection for along-street and across-street roof-top winds respectively. Results also indicate that for oblique rooftop flows, the intersection flow is a complex combination of bifurcated channelled flows, recirculation and corner vortices. Asymmetries in local building geometry around the intersection and small changes in the background wind direction (changes in 15-min mean θref of 5–10 degrees) were also observed to have profound influences on the behaviour of intersection flow patterns. Consequently, short time-scale variability in the background flow direction can lead to highly scattered in-street mean flow angles masking the true multi-modal features of the flow and thus further complicating modelling challenges.

Costs to farmers of a tuberculosis breakdown

An on-farm survey of 151 cattle farmers who had experienced a bovine tuberculosis (Mycobacterium bovis) breakdown on their farms was undertaken in 2003 to assess the costs associated with the breakdown. In 90 per cent of cases the cost was estimated to be less than 18,513 pound for dairy herds and less than El 1,462 for beef herds, but with a range from 229 pound to 103,817 pound. The main cost was the slaughter of reactor cattle. For the majority of the farmers, the compensation payments seemed to meet most of the costs of their breakdowns, although a majority was still left with net losses.

Unravelling the conundrum of tannins in animal nutrition and health

This paper examines the nutritional and veterinary effects of tannins on ruminants and makes some comparisons with non-ruminants. Tannin chemistry per se is not covered and readers are referred to several excellent reviews instead: (a) Okuda T et al. Heterocycles 30:1195-1218 (1990); (b) Ferreira D and Slade D. Nat Prod Rep 19:517-541 (2002); (c) Yoshida T et al. In Studies in Natural Product Chemistry. Elsevier Science, Amsterdam, pp. 395-453 (2000); (d) Khanbabaee K and van Ree T. Nat Prod Rep 18:641-649 (2001); (e) Okuda et al. Phytochemistvy 55:513-529 (2000). The effects of tannins on rumen micro-organisms are also not reviewed, as these have been addressed by others: (a) McSweeney CS et al. Anim Feed Sci Technol 91:83-93 (2001); (b) Smith AH and Mackie RI. Appl Environ Microbiol 70:1104-1115 (2004). This paper deals first with the nutritional effects of tannins in animal feeds, their qualitative and quantitative diversity, and the implications of tannin-protein complexation. It then summarises the known physiological and harmful effects and discusses the equivocal evidence of the bioavailability of tannins. Issues concerning tannin metabolism and systemic effects are also considered. Opportunities are presented on how to treat feeds with high tannin contents, and some lesser-known but successful feeding strategies are highlighted. Recent research has explored the use of tannins for preventing animal deaths from bloat, for reducing intestinal parasites and for lowering gaseous ammonia and methane emissions. Finally, several tannin assays and a hypothesis are discussed that merit further investigation in order to assess their suitability for predicting animal responses. The aim is to provoke discussion and spur readers into new approaches. An attempt is made to synthesise the emerging information for relating tannin structures with their activities. Although many plants with high levels of tannins produce negative effects and require treatments, others are very useful animal feeds. Our ability to predict whether tannin-containing feeds confer positive or negative effects will depend on interdisciplinary research between animal nutritionists and plant chemists. The elucidation of tannin structure-activity relationships presents exciting opportunities for future feeding strategies that will benefit ruminants and the environment within the contexts of extensive, semi-intensive and some intensive agricultural systems. (c) 2006 Society of Chemical Industry

Unravelling the conundrum of tannins in animal nutrition and health

This paper examines the nutritional and veterinary effects of tannins on ruminants and makes some comparisons with non-ruminants. Tannin chemistry per se is not covered and readers are referred to several excellent reviews instead: (a) Okuda T et al. Heterocycles 30:1195-1218 (1990); (b) Ferreira D and Slade D. Nat Prod Rep 19:517-541 (2002); (c) Yoshida T et al. In Studies in Natural Product Chemistry. Elsevier Science, Amsterdam, pp. 395-453 (2000); (d) Khanbabaee K and van Ree T. Nat Prod Rep 18:641-649 (2001); (e) Okuda et al. Phytochemistvy 55:513-529 (2000). The effects of tannins on rumen micro-organisms are also not reviewed, as these have been addressed by others: (a) McSweeney CS et al. Anim Feed Sci Technol 91:83-93 (2001); (b) Smith AH and Mackie RI. Appl Environ Microbiol 70:1104-1115 (2004). This paper deals first with the nutritional effects of tannins in animal feeds, their qualitative and quantitative diversity, and the implications of tannin-protein complexation. It then summarises the known physiological and harmful effects and discusses the equivocal evidence of the bioavailability of tannins. Issues concerning tannin metabolism and systemic effects are also considered. Opportunities are presented on how to treat feeds with high tannin contents, and some lesser-known but successful feeding strategies are highlighted. Recent research has explored the use of tannins for preventing animal deaths from bloat, for reducing intestinal parasites and for lowering gaseous ammonia and methane emissions. Finally, several tannin assays and a hypothesis are discussed that merit further investigation in order to assess their suitability for predicting animal responses. The aim is to provoke discussion and spur readers into new approaches. An attempt is made to synthesise the emerging information for relating tannin structures with their activities. Although many plants with high levels of tannins produce negative effects and require treatments, others are very useful animal feeds. Our ability to predict whether tannin-containing feeds confer positive or negative effects will depend on interdisciplinary research between animal nutritionists and plant chemists. The elucidation of tannin structure-activity relationships presents exciting opportunities for future feeding strategies that will benefit ruminants and the environment within the contexts of extensive, semi-intensive and some intensive agricultural systems. (c) 2006 Society of Chemical Industry

A cross-sectional study of reproductive performance of smallholder dairy cows in coastal Tanzania

A retrospective cross-sectional study was conducted on 200 randomly selected smallholder farms from a mixed dairy farming system in Tanga, Tanzania, between January and April 1999. We estimated the frequency and determinants of long calving interval (LCI), retention of fetal membrane (RFM), dystocia, and abortion in smallholder crossbred cattle and explored birth trends. The mean calving interval was 500 days and birth rate was 65 per 100 cow-years. Dystocia was reported to affect 58% of calvings, and 17.2% of animals suffered RFM. Using mixed effect models, the variables associated with LCI, RFM and dystocia were breed, level of exotic blood and condition score. Zebu breeding was associated with LCI (odds ratio (OR) = 2.3, p = 0.041) and Friesian breeding with lower odds for RF (OR = 0.26, p = 0.020). Animals with higher levels of exotic blood had lower odds for evidence of dystocia (OR = 0.45, p = 0.021). Evidence of dystocia was significantly associated with poor condition score (beta = -1.10, p = 0.001). Our observations suggest that LCIs are common in smallholder dairy farms in this region and a likely source of economic loss. Dystocia, RFM, poor condition score and mineral deficiency were common problems and were possibly linked to LCI.

Nuclear magnetic resonance structure shows that the severe acute respiratory syndrome coronavirus-unique domain contains a macrodomain fold

The nuclear magnetic resonance (NMR) structure of a central segment of the previously annotated severe acute respiratory syndrome (SARS)-unique domain (SUD-M, for "middle of the SARS-unique domain") in SARS coronavirus (SARS-CoV) nonstructural protein 3 (nsp3) has been determined. SUD-M(513-651) exhibits a macrodomain fold containing the nsp3 residues 528 to 648, and there is a flexibly extended N-terminal tail with the residues 513 to 527 and a C-terminal flexible tail of residues 649 to 651. As a follow-up to this initial result, we also solved the structure of a construct representing only the globular domain of residues 527 to 651 [SUD-M(527-651)]. NMR chemical shift perturbation experiments showed that SUD-M(527-651) binds single-stranded poly(A) and identified the contact area with this RNA on the protein surface, and electrophoretic mobility shift assays then confirmed that SUD-M has higher affinity for purine bases than for pyrimidine bases. In a further search for clues to the function, we found that SUD-M(527-651) has the closest three-dimensional structure homology with another domain of nsp3, the ADP-ribose-1 ''-phosphatase nsp3b, although the two proteins share only 5% sequence identity in the homologous sequence regions. SUD-M(527-651) also shows three-dimensional structure homology with several helicases and nucleoside triphosphate-binding proteins, but it does not contain the motifs of catalytic residues found in these structural homologues. The combined results from NMR screening of potential substrates and the structure-based homology studies now form a basis for more focused investigations on the role of the SARS-unique domain in viral infection.

NMR structure shows that the SARS-unique domain contains a macrodomain fold

The NMR structure of a central segment of the previously annotated "SARS-unique domain" (SUD-M; "middle of the SARS-unique domain") in the SARS coronavirus (SARS-CoV) non-structural protein 3 (nsp3) has been determined. SUD-M(513-651) exhibits a macrodomain fold containing the nsp3-residues 528-648, and there is a flexibly extended N-terminal tail with the residues 513-527 and a C-terminal flexible tail of residues 649-651. As a follow-up to this initial result, we also solved the structure of a construct representing only the globular domain of residues 527-651 [SUD-M(527-651)]. NMR chemical shift perturbation experiments showed that SUD-M(527-651) binds single-stranded poly-A and identified the contact area with this RNA on the protein surface, and electrophoretic mobility shift assays then confirmed that SUD-M has higher affinity for purine bases than for pyrimidine bases. In further search for clues to the function, we found that SUD-M(527-651) has the closest three-dimensional structure homology with another domain of nsp3, the ADP-ribose-1''-phosphatase nsp3b, although the two proteins share only 5% sequence identity in the homologous sequence regions. SUD-M(527-651) also shows 3D structure homology with several helicases and NTP-binding proteins, but it does not contain the motifs of catalytic residues found in these structural homologues. The combined results from NMR screening of potential substrates and the structure-based homology studies now form a basis for more focused investigations on the role of the SARS-unique domain in viral infection.

An entropy-based financial decision support system (e-FDSS) for project analysis in construction SMEs

Uncertainty contributes a major part in the accuracy of a decision-making process while its inconsistency is always difficult to be solved by existing decision-making tools. Entropy has been proved to be useful to evaluate the inconsistency of uncertainty among different respondents. The study demonstrates an entropy-based financial decision support system called e-FDSS. This integrated system provides decision support to evaluate attributes (funding options and multiple risks) available in projects. Fuzzy logic theory is included in the system to deal with the qualitative aspect of these options and risks. An adaptive genetic algorithm (AGA) is also employed to solve the decision algorithm in the system in order to provide optimal and consistent rates to these attributes. Seven simplified and parallel projects from a Hong Kong construction small and medium enterprise (SME) were assessed to evaluate the system. The result shows that the system calculates risk adjusted discount rates (RADR) of projects in an objective way. These rates discount project cash flow impartially. Inconsistency of uncertainty is also successfully evaluated by the use of the entropy method. Finally, the system identifies the favourable funding options that are managed by a scheme called SME Loan Guarantee Scheme (SGS). Based on these results, resource allocation could then be optimized and the best time to start a new project could also be identified throughout the overall project life cycle.

Proteomic analysis of the site specificity of glycation and carboxymethylation of ribonuclease

Proteomic analysis using electrospray liquid chromatography-mass spectrometry (ESI-LC-MS) has been used to compare the sites of glycation (Amadori adduct formation) and carboxymethylation of RNase and to assess the role of the Amadori adduct in the formation of the advanced glycation end-product (AGE), N-is an element of-(carboxymethyl)lysine (CIVIL). RNase (13.7 mg/mL, 1 mM) was incubated with glucose (0.4 M) at 37 degreesC for 14 days in phosphate buffer (0.2 M, pH 7.4) under air. On the basis of ESI-LC-MS of tryptic peptides, the major sites of glycation of RNase were, in order, K41, K7, K1, and K37. Three of these, in order, K41, K7, and K37 were also the major sites of CIVIL formation. In other experiments, RNase was incubated under anaerobic conditions (1 mM DTPA, N-2 purged) to form Amadori-modified protein, which was then incubated under aerobic conditions to allow AGE formation. Again, the major sites of glycation were, in order, K41, K7, K1, and K37 and the major sites of carboxymethylation were K41, K7, and K37. RNase was also incubated with 1-5 mM glyoxal, substantially more than is formed by autoxidation of glucose under experimental conditions, but there was only trace modification of lysine residues, primarily at K41. We conclude the following: (1) that the primary route to formation of CIVIL is by autoxidation of Amadori adducts on protein, rather than by glyoxal generated on autoxidation of glucose; and (2) that carboxymethylation, like glycation, is a site-specific modification of protein affected by neighboring amino acids and bound ligands, such as phosphate or phosphorylated compounds. Even when the overall extent of protein modification is low, localization of a high proportion of the modifications at a few reactive sites might have important implications for understanding losses in protein functionality in aging and diabetes and also for the design of AGE inhibitors.

Saccadic eye movements as an index of perceptual decision-making

One of the most common decisions we make is the one about where to move our eyes next. Here we examine the impact that processing the evidence supporting competing options has on saccade programming. Participants were asked to saccade to one of two possible visual targets indicated by a cloud of moving dots. We varied the evidence which supported saccade target choice by manipulating the proportion of dots moving towards one target or the other. The task was found to become easier as the evidence supporting target choice increased. This was reflected in an increase in percent correct and a decrease in saccade latency. The trajectory and landing position of saccades were found to deviate away from the non-selected target reflecting the choice of the target and the inhibition of the non-target. The extent of the deviation was found to increase with amount of sensory evidence supporting target choice. This shows that decision-making processes involved in saccade target choice have an impact on the spatial control of a saccade. This would seem to extend the notion of the processes involved in the control of saccade metrics beyond a competition between visual stimuli to one also reflecting a competition between options.

Quantification of boundary definition using pulsed terahertz radiation for wedged geometries

The interaction of a terahertz beam with a sample containing a material boundary across the profile of the terahertz beam produces characteristic spectroscopic detail. A full vectorial model is presented to quantify boundary definition for a series of wedged geometries. As a result of this work, using simple geometric forms, we wish to be able to extend these ideas to characterize boundaries in more irregular samples, impacting most application areas of pulsed terahertz radiation.