Repeated challenge with prion disease: The risk of infection and impact on incubation period

Natural exposure to prion disease is likely to occur throughout successive challenges, yet most experiments focus on single large doses of infectious material. We analyze the results from an experiment in which rodents were exposed to multiple doses of feed contaminated with the scrapie agent. We formally define hypotheses for how the doses combine in terms of statistical models. The competing hypotheses are that only the total dose of infectivity is important (cumulative model), doses act independently, or a general alternative that interaction between successive doses occurs (to raise or lower the risk of infection). We provide sample size calculations to distinguish these hypotheses. In the experiment, a fixed total dose has a significantly reduced probability of causing infection if the material is presented as multiple challenges, and as the time between challenges lengthens. Incubation periods are shorter and less variable if all material is consumed on one occasion. We show that the probability of infection is inconsistent with the hypothesis that each dose acts as a cumulative or independent challenge. The incubation periods are inconsistent with the independence hypothesis. Thus, although a trend exists for the risk of infection with prion disease to increase with repeated doses, it does so to a lesser degree than is expected if challenges combine independently or in a cumulative manner.

Over-parameterised, uncertain 'mathematical marionettes' - How can we best use catchment water quality models? An example of an 80-year catchment-scale nutrient balance

The Integrated Catchment Model of Nitrogen (INCA-N) was applied to the River Lambourn, a Chalk river-system in southern England. The model's abilities to simulate the long-term trend and seasonal patterns in observed stream water nitrate concentrations from 1920 to 2003 were tested. This is the first time a semi-distributed, daily time-step model has been applied to simulate such a long time period and then used to calculate detailed catchment nutrient budgets which span the conversion of pasture to arable during the late 1930s and 1940s. Thus, this work goes beyond source apportionment and looks to demonstrate how such simulations can be used to assess the state of the catchment and develop an understanding of system behaviour. The mass-balance results from 1921, 1922, 1991, 2001 and 2002 are presented and those for 1991 are compared to other modelled and literature values of loads associated with nitrogen soil processes and export. The variations highlighted the problem of comparing modelled fluxes with point measurements but proved useful for identifying the most poorly understood inputs and processes thereby providing an assessment of input data and model structural uncertainty. The modelled terrestrial and instream mass-balances also highlight the importance of the hydrological conditions in pollutant transport. Between 1922 and 2002, increased inputs of nitrogen from fertiliser, livestock and deposition have altered the nitrogen balance with a shift from possible reduction in soil fertility but little environmental impact in 1922, to a situation of nitrogen accumulation in the soil, groundwater and instream biota in 2002. In 1922 and 2002 it was estimated that approximately 2 and 18 kg N ha(-1) yr(-1) respectively were exported from the land to the stream. The utility of the approach and further considerations for the best use of models are discussed. (C) 2008 Elsevier B.V. All rights reserved.

Influence of sodium chloride on seed germination and seedling root growth of cotton (Gossypium hirsutum L.)

Response of cotton (Gossypium hirsutum L. cv. NIAB-78) to salinity, in terms of seed germination, seedling root growth and root Na+ and K+ content was determined in a laboratory experiment. Cotton seeds were exposed to increasing salinity levels using germination water with Sodium chloride concentrations of 0, 50, 100, 150 and 200 mM, to provide different degrees of salt stress. Germinated seeds were counted and roots were harvested at 24, 48, 72 and 96 h after the start of the experiment. It appeared that seed germination was only slightly affected by an increase in salinity (in most cases the differences between treatment were non-significant), whereas root length, root growth rate, root fresh and dry weights were severely affected, generally highly significant differences in these variables were found for comparisons involving most combinations of salinity levels, in particular with increased incubation period. K+ contents decreased with increasing salinity levels, although differences in K+ content were only significant when comparing the control and the 4 salinity levels. Na+ content of the roots increased with increasing levels of NaCl in the germination water, suggesting an exchange of K+ for Na+. The ratio K+/Na+ strongly decreased with rising levels of salinity from around 4.5 for the control to similar to 1 at 200 mM NaCl.

Over-parameterised, uncertain 'mathematical marionettes' - How can we best use catchment water quality models? An example of an 80-year catchment-scale nutrient balance

The Integrated Catchment Model of Nitrogen (INCA-N) was applied to the River Lambourn, a Chalk river-system in southern England. The model's abilities to simulate the long-term trend and seasonal patterns in observed stream water nitrate concentrations from 1920 to 2003 were tested. This is the first time a semi-distributed, daily time-step model has been applied to simulate such a long time period and then used to calculate detailed catchment nutrient budgets which span the conversion of pasture to arable during the late 1930s and 1940s. Thus, this work goes beyond source apportionment and looks to demonstrate how such simulations can be used to assess the state of the catchment and develop an understanding of system behaviour. The mass-balance results from 1921, 1922, 1991, 2001 and 2002 are presented and those for 1991 are compared to other modelled and literature values of loads associated with nitrogen soil processes and export. The variations highlighted the problem of comparing modelled fluxes with point measurements but proved useful for identifying the most poorly understood inputs and processes thereby providing an assessment of input data and model structural uncertainty. The modelled terrestrial and instream mass-balances also highlight the importance of the hydrological conditions in pollutant transport. Between 1922 and 2002, increased inputs of nitrogen from fertiliser, livestock and deposition have altered the nitrogen balance with a shift from possible reduction in soil fertility but little environmental impact in 1922, to a situation of nitrogen accumulation in the soil, groundwater and instream biota in 2002. In 1922 and 2002 it was estimated that approximately 2 and 18 kg N ha(-1) yr(-1) respectively were exported from the land to the stream. The utility of the approach and further considerations for the best use of models are discussed. (C) 2008 Elsevier B.V. All rights reserved.

Low density lipoprotein undergoes oxidation within lysosomes in cells

The oxidised low density lipoprotein (LDL) hypothesis of atherosclerosis proposes that LDL undergoes oxidation in the interstitial fluid of the arterial wall. We have shown that aggregated (vortexed) nonoxidised LDL was taken up by J774 mouse macrophages and human monocyte-derived macrophages and oxidised intracellularly, as assessed by the microscopic detection of ceroid, an advanced lipid oxidation product. Confocal microscopy showed that the ceroid was located in the lysosomes. To confirm these findings, J774 macrophages were incubated with acetylated LDL, which is internalised rapidly to lysosomes, and then incubated (chase incubation) in the absence of any LDL. The intracellular levels of oxysterols, measured by HPLC, increased during the chase incubation period, showing that LDL must have been oxidised inside the cells. Furthermore, we found that this oxidative modification was inhibited by lipid-soluble antioxidants, an iron chelator taken up by fluid-phase pinocytosis and the lysosomotropic drug chloroquine, which increases the pH of lysosomes. The results indicate that LDL oxidation can occur intracellularly, most probably within lysosomes.

Phases of dormancy in yam tubers (Dioscorea rotundata)

center dot Background and Aims The control of dormancy in yam (Disocorea spp.) tubers is poorly understood and attempts to shorten the long dormant period (i.e. cause tubers to sprout or germinate much earlier) have been unsuccessful. The aim of this study was to identify and define the phases of dormancy in Dioscorea rotundata tubers, and to produce a framework within which dormancy can be more effectively studied. center dot Methods Plants of 'TDr 131' derived from tissue culture were grown in a glasshouse simulating temperature and photoperiod at Ibadan (7 degrees N), Nigeria to produce tubers. Tubers were sampled on four occasions: 30 d before shoot senescence (149 days after planting, DAP), at shoot senescence (179 DAP), and twice during storage at a constant 25 degrees C (269 and 326 DAP). The development of the apical shoot bud was described from tissue sections. In addition, the responsiveness of shoot apical bud development to plant growth regulators (gibberellic acid, 2-chloroethanol and thiourea) applied to excised tuber sections was also examined 6 and 12 d after treatment. center dot Key Results and Conclusions Three phases of tuber dormancy are proposed: Phase I, from tuber initiation to the appearance of the tuber germinating meristem; Phase II, from the tuber germinating meristem to initiation of foliar primordium; and Phase III, from foliar primordium to appearance of the shoot bud on the surface of the tuber. Phase I is the longest phase (approx. 220 d in 'TDr 131'), is not affected by PGRs and is proposed to be an endo-dormant phase. Phases II and III are shorter (< 70 d in total), are influenced by PGRs and environmental conditions, and are therefore endo-/eco-dormant phases. To manipulate dormancy to allow off-season planting and more than one generation per year requires that the duration of Phase I is shortened.

Chemical composition and in vitro fermentation of tannin-rich tree fruits

Dry and mature tree fruits are a potential source of protein for goats in the semi-arid areas of southern Africa, but their chemical composition and feeding value is largely unknown. This study presents the chemical composition and in vitro fermentation of indehiscent whole fruits and separated seed and hull fractions from Acacia nilotica, Acacia erubescens, Acacia sieberiana, Acacia erioloba, Piliostigma thonningii and Dichrostachys cinerea trees. Results indicate that the N contents of whole fruits ranged between 13.5 g/kg DM (A. nilotica) and 27.1 g/kg DM (A. erubescens). Seeds had a higher N content than hulls for all tree species. A. nilotica, D. cinerea and P thonningii fruits had high levels of extractable phenolics (758, 458 and 299 g/kg DM, respectively). Soluble phenolics (SPh) and ytterbium precipitable phenolics (YbPh) levels were negatively correlated to in vitro gas production but positively correlated to in vitro organic matter degradability (iOMD). Partition factors for whole fruits at 48 h ranged between 3.6 mg/ml for A. erioloba and 7.8 mg/ml for A. nilotica. Seeds of A. erioloba, A. erubescens and P thonningii were consistently fermented more efficiently throughout the incubation period compared to their whole fruits or hulls. Estimating in vitro degradability of phenolic-rich substrates through filtration procedures can give erroneous results due to the loss of soluble phenolics, which are not necessarily degradable. The feeding value of fruits from D. cinerea and A. nilotica tree species may be reduced due to the presence of high levels of phenolics. (C) 2007 Elsevier B.V. All rights reserved.

Low density lipoprotein undergoes oxidation within lysosomes in cells

The oxidized low density lipoprotein (LDL) hypothesis of atherosclerosis proposes that LDL undergoes oxidation in the interstitial fluid of the arterial wall. We have shown that aggregated (vortexed) nonoxidized LDL was taken up by J774 mouse macrophages and human monocyte-derived macrophages and oxidized intracellularly, as assessed by the microscopic detection of ceroid, an advanced lipid oxidation product. Confocal microscopy showed that the ceroid was located in the lysosomes. To confirm these findings, J774 macrophages were incubated with acetylated LDL, which is internalized rapidly to lysosomes, and then incubated (chase incubation) in the absence of any LDL. The intracellular levels of oxysterols, measured by HPLC, increased during the chase incubation period, showing that LDL must have been oxidized inside the cells. Furthermore, we found that this oxidative modification was inhibited by lipid-soluble antioxidants, an iron chelator taken up by fluid-phase pinocytosis and the lysosomotropic drug chloroquine, which increases the pH of lysosomes. The results indicate that LDL oxidation can occur intracellularly, most probably within lysosomes.

Phases of dormancy in yam tubers (Dioscorea rotundata)

Background and Aims The control of dormancy in yam (Disocorea spp.) tubers is poorly understood and attempts to shorten the long dormant period (i.e. cause tubers to sprout or germinate much earlier) have been unsuccessful. The aim of this study was to identify and define the phases of dormancy in Dioscorea rotundata tubers, and to produce a framework within which dormancy can be more effectively studied. center dot Methods Plants of 'TDr 131' derived from tissue culture were grown in a glasshouse simulating temperature and photoperiod at Ibadan (7 degrees N), Nigeria to produce tubers. Tubers were sampled on four occasions: 30 d before shoot senescence (149 days after planting, DAP), at shoot senescence (179 DAP), and twice during storage at a constant 25 degrees C (269 and 326 DAP). The development of the apical shoot bud was described from tissue sections. In addition, the responsiveness of shoot apical bud development to plant growth regulators (gibberellic acid, 2-chloroethanol and thiourea) applied to excised tuber sections was also examined 6 and 12 d after treatment. center dot Key Results and Conclusions Three phases of tuber dormancy are proposed: Phase I, from tuber initiation to the appearance of the tuber germinating meristem; Phase II, from the tuber germinating meristem to initiation of foliar primordium; and Phase III, from foliar primordium to appearance of the shoot bud on the surface of the tuber. Phase I is the longest phase (approx. 220 d in 'TDr 131'), is not affected by PGRs and is proposed to be an endo-dormant phase. Phases II and III are shorter (< 70 d in total), are influenced by PGRs and environmental conditions, and are therefore endo-/eco-dormant phases. To manipulate dormancy to allow off-season planting and more than one generation per year requires that the duration of Phase I is shortened.

Back from beyond the bid-ask spread: perspectives on liquidity

Research into the topic of liquidity has greatly benefited from the availability of data. Although bid-ask spreads were inaccessible to researchers, Roll (1984) provided a conceptual model that estimated the effective bid-ask prices from regular time series data, recorded on a daily or longer interval. Later data availability improved and researchers were able to address questions regarding the factors that influenced the spreads and the relationship between spreads and risk, return and liquidity. More recently transaction data have been used to measure the effective spread and researchers have been able to refine the concepts of liquidity to include the impact of transactions on price movements (Clayton and McKinnon, 2000) on a trade-by-trade analysis. This paper aims to use techniques that combine elements from all three approaches and, by studying US data over a relatively long time period, to throw light on earlier research as well as to reveal the changes in liquidity over the period controlling for extraneous factors such as market, age and size of REIT. It also reveals some comparable results for the UK market over the same period.

Synoptic-scale controls of persistent low temperature and icy weather over southern China in January 2008

In January 2008, central and southern China experienced persistent low temperatures, freezing rain, and snow. The large-scale conditions associated with the occurrence and development of these snowstorms are examined in order to identify the key synoptic controls leading to this event. Three main factors are identified: 1) the persistent blocking high over Siberia, which remained quasi-stationary around 65°E for 3 weeks, led to advection of dry and cold Siberian air down to central and southern China; 2) a strong persistent southwesterly flow associated with the western Pacific subtropical high led to enhanced moisture advection from the Bay of Bengal into central and southern China; and 3) the deep inversion layer in the lower troposphere associated with the extended snow cover over most of central and southern China. The combination of these three factors is likely responsible for the unusual severity of the event, and hence a long return period

Success and failure of grassroots innovations for addressing climate change: the case of the Transition Movement

Grassroots innovations emerge as networks generating innovative solutions for climate change adaptation and mitigation. However, it is unclear if grassroots innovations can be successful in responding to climate change. Little evidence exists on replication, international comparisons are rare, and research tends to overlook discontinued responses in favour of successful ones. We take the Transition Movement as a case study of a rapidly spreading transnational grassroots network, and include both active and non-active local transition initiatives. We investigate the replication of grassroots innovations in different contexts with the aim to uncover general patterns of success and failure, and identify questions for future research. An online survey was carried out in 23 countries (N=276). The data analysis entailed testing the effect of internal and contextual factors of success as drawn from the existing literature, and the identification of clusters of transition initiatives with similar internal and contextual factor configurations. Most transition initiatives consider themselves successful. Success is defined along the lines of social connectivity and empowerment, and external environmental impact. We find that less successful transition initiatives might underestimate the importance of contextual factors and material resources in influencing success. We also find that their diffusion is linked to the combination of local-global learning processes, and that there is an incubation period during which a transition initiative is consolidated. Transition initiatives seem capable of generalising organisational principles derived from unique local experiences that seem to be effective in other local contexts. However, the geographical locations matter with regard to where transition initiatives take root and the extent of their success, and ‘place attachment’ may have a role in the diffusion of successful initatives. We suggest that longitudinal comparative studies can advance our understanding in this regard, as well as inform the changing nature of the definition of success at different stages of grassroots innovation development, and the dynamic nature of local and global linkages.

Does ochre have the potential to be a remedial treatment for As-contaminated soils?

Ochre is an iron oxyhydroxide-rich waste that accumulates in water bodies associated with disused mines. Laboratory experiments were conducted to examine the potential of four different ochres to be used as remedial agents for As contaminated soils. The ochres removed As from solution (200 and 500 mg L−1) in adsorption experiments at pH 3 and 8 and, when added to As contaminated soil (5% w/w) significantly reduced As release to solution. In both these experiments the highest surface area ochres performed best. The impact of ochre amendments on uptake of As from soil by plants and humans and release of As to ground water was assessed in a year-long incubation study. Ochres increased soil pH and reduced CaCl2 extractable As but had no consistent effect on plant growth, plant As uptake or As extraction in physiologically-based extraction tests. Ochre may be better used for water treatment than soil remediation.

Spatial evaluation of volcanic ash forecasts using satellite observations

The decision to close airspace in the event of a volcanic eruption is based on hazard maps of predicted ash extent. These are produced using output from volcanic ash transport and dispersion (VATD)models. In this paper an objectivemetric to evaluate the spatial accuracy of VATD simulations relative to satellite retrievals of volcanic ash is presented. The 5 metric is based on the fractions skill score (FSS). Thismeasure of skill provides more information than traditional point-bypoint metrics, such as success index and Pearson correlation coefficient, as it takes into the account spatial scale overwhich skill is being assessed. The FSS determines the scale overwhich a simulation has skill and can differentiate between a "near miss" and a forecast that is badly misplaced. The 10 idealised scenarios presented show that even simulations with considerable displacement errors have useful skill when evaluated over neighbourhood scales of 200–700km2. This method could be used to compare forecasts produced by different VATDs or using different model parameters, assess the impact of assimilating satellite retrieved ash data and evaluate VATD forecasts over a long time period.

Temperature affects microbial decomposition of cadavers (Rattus rattus) in contrasting soils

The ecology of soils associated with dead mammals (i.e. cadavers) is poorly understood. Although temperature and soil type are well known to influence the decomposition of other organic resource patches, the effect of these variables on the degradation of cadavers in soil has received little experimental investigation. To address this, cadavers of juvenile rats (Rattus rattus) were buried in one of three contrasting soils (Sodosol, Rudosol, and Vertosol) from tropical savanna ecosystems in Queensland, Australia and incubated at 29 °C, 22 °C, or 15 °C in a laboratory setting. Cadavers and soils were destructively sampled at intervals of 7 days over an incubation period of 28 days. Measurements of decomposition included cadaver mass loss, carbon dioxide–carbon (CO2–C) evolution, microbial biomass carbon (MBC), protease activity, phosphodiesterase activity, and soil pH, which were all significantly positively affected by cadaver burial. A temperature effect was observed where peaks or differences in decomposition that at occurred at higher temperature would occur at later sample periods at lower temperature. Soil type also had an important effect on some measured parameters. These findings have important implications for a largely unexplored area of soil ecology and nutrient cycling, which are significant for forensic science, cemetery planning and livestock carcass disposal.