Nitrogen-15 and Oxygen-18 Natural Abundance of Potassium Chloride Extractable Soil Nitrate Using the Denitrifier Method

In agroecosystems, most isotopic investigations of NO3- involve the use of tracers that are artificially enriched in 15N. Although the dual isotope composition of NO3-— d15N and d18O is especially beneficial for understanding the origin and fate of NO3-, its use for KCl-extractable soil NO3- has been hampered by the lack of a suitable analytical technique. Our objective was to test whether the denitrifier method, whereby NO3- is reduced to N2O before mass spectrometric analysis, can be used to determine the N and O isotopic composition of NO3- from 2 M KCl soil extracts. Several internationally accepted NO3- standards were dissolved in 2 M KCl, the conventional extractant for soil inorganic N, and inoculated with the bacterial strain Pseudomonas aureofaciens (ATCC no. 13985). The standard deviation of the NO3- standards analyzed did not exceed 0.2‰ for d15N and 0.3‰ for d18O values. After appropriate corrections, differences between our measured and consensus d15N and d18O values of standard NO3- generally were within the standard deviations given for the consensus values. Both d15N and d18O values were reproducible among separate analytical runs. The method was also tested on genuine 2 M KCl extracts from unfertilized and fertilized soils. Depending on N fertilization, the soils had distinct d15N and d18O values, which were attributed to amendment with NH4NO3 fertilizer. Hence, our data indicate that the denitrifier method provides a fast, reliable, precise, and accurate way of simultaneously analyzing the natural abundances of 15N and 18O in KCl-extractable soil NO3-.

Metabolism of Maillard reaction products by the human gut microbiota - implications for health

The human colonic microbiota imparts metabolic versatility on the colon, interacts at many levels in healthy intestinal and systemic metabolism, and plays protective roles in chronic disease and acute infection. Colonic bacterial metabolism is largely dependant on dietary residues from the upper gut. Carbohydrates, resistant to digestion, drive colonic bacterial fermentation and the resulting end products are considered beneficial. Many colonic species ferment proteins but the end products are not always beneficial and include toxic compounds, such as amines and phenols. Most components of a typical Western diet are heat processed. The Maillard reaction, involving food protein and sugar, is a complex network of reactions occurring during thermal processing. The resultant modified protein resists digestion in the small intestine but is available for colonic bacterial fermentation. Little is known about the fate of the modified protein but some Maillard reaction products (MRP) are biologically active by, e.g. altering bacterial population levels within the colon or, upon absorption, interacting with human disease mechanisms by induction of inflammatory responses. This review presents current understanding of the interactions between MRP and intestinal bacteria. Recent scientific advances offering the possibility of elucidating the consequences of microbe-MRP interactions within the gut are discussed.

Valuing the cultural monuments of Armenia: Bayesian updating of prior beliefs in contingent valuation

The most appropriate way to measure the social benefits of conserving built cultural heritage sites is to ask the beneficiaries of conservation interventions how much they would be willing to pay for them. We use contingent valuation - a survey-based approach that elicits willingness to pay (WTP) directly from individuals - to estimate the benefits of a nationwide conservation of built cultural heritage sites in Armenia. The survey was administered to Armenian nationals living in Armenia, and obtained extensive information about the respondents' perceptions of the current state of conservation of monuments in Armenia, described the current situation, presented a hypothetical conservation program, elicited WTP for it, and queried individuals about what they thought would happen to monument sites in the absence of the government conservation program. We posit that respondents combined the information about the fate of monuments provided by the questionnaire with their prior beliefs, and that WTP for the good, or program, is likely to be affected by these updated beliefs. We propose a Bayesian updating model of prior beliefs, and empirically implement it with the data from our survey. We found that uncertainty about what would happen to monuments in the absence of the program results in lower WTP amounts. © 2008 Pion Ltd and its Licensors.

Quantification of nanoparticle uptake by cells using microscopical and analytical techniques

Quantification of nanoparticles in biological systems (i.e., cells, tissues and organs) is becoming a vital part of nanotoxicological and nanomedical fields. Dose is a key parameter when assessing behavior and any potential risk of nanomaterials. Various techniques for nanoparticle quantification in cells and tissues already exist but will need further development in order to make measurements reliable, reproducible and intercomparable between different techniques. Microscopy allows detection and location of nanoparticles in cells and has been used extensively in recent years to characterize nanoparticles and their pathways in living systems. Besides microscopical techniques (light microscopy and electron microscopy mainly), analytical techniques such as mass spectrometry, an established technique in trace element analysis, have been used in nanoparticle research. Other techniques require 'labeled particles, fluorescently, radioactively or magnetically. However, these techniques lack spatial resolution and subcellular localization is not possible. To date, only electron microscopy offers the resolving power to determine accumulation of nanoparticles in cells due to its ability to image particles individually. So-called super-resolution light microscopy techniques are emerging to provide sufficient resolution on the light microscopy level to image or 'see particles as individual particles. Nevertheless, all microscopy techniques require statistically sound sampling strategies in order to provide quantitative results. Stereology is a well-known sampling technique in various areas and, in combination with electron microscopy, proves highly successful with regard to quantification of nanoparticle uptake by cells. © 2010 Future Medicine Ltd.

Characterization of Numb expression in astrocytomas

During early neurodevelopment, asymmetric segregation of Numb in mitotic progenitor cells influences the fate of daughter cells, whereby one daughter retains the progenitor phenotype while the other proceeds along a differentiation pathway. Numb has also been reported to function as a tumor suppressor in breast cancers and medulloblastomas. Given its role in maintaining neural progenitor pools in animal models and its reported role as a tumor suppressor, Numb could potentially contribute to astrocytoma oncogenesis. We characterized Numb expression in both human astrocytoma tissue samples and glioblastoma cell lines. We found that Numb is expressed in all grades of astrocytomas, being predominantly cytoplasmic in higher-grade astrocytomas but nuclear in pilocytic astrocytomas. Numb is also present in normal neurons, but not in normal astrocytes. In cultured glioblastoma cells, Numb concentrates in the perinuclear region and process tips. Numb expression in astrocytomas recapitulates that of progenitor cells during neurodevelopment, and suggests a role for Numb in astrocytoma oncogenesis.

Antibody-targeted nanoparticles for cancer therapy

In recent years, nanoparticulate-mediated drug delivery research has examined a full spectrum of nanoparticles that can be used in diagnostic and therapeutic cancer applications. A key aspect of this technology is in the potential to specifically target the nanoparticles to diseased cells using a range of molecules, in particular antibodies. Antibody-nanoparticle conjugates have the potential to elicit effective targeting and release of therapeutic targets at the disease site, while minimizing off-target side effects caused by dosing of normal tissues. This article provides an overview of various antibody-conjugated nanoparticle strategies, focusing on the rationale of cell-surface receptors targeted and their potential clinical application.

Spatio-temporal analysis of DNA damage repair using the X-ray microbeam

Cellular response to radiation damage is made by a complex network of pathways and feedback loops whose spatiotemporal organization is still unclear despite its decisive role in determining the fate of the damaged cell. The single-cell approach and the high spatial resolution offered by microbeams provide the perfect tool to study and quantify the dynamic processes associated with the induction and repair of DNA damage. The soft X-ray microbeam has been used to follow the development of radiation induced foci in live cells by monitoring their size and intensity as a function of dose and time using yellow fluorescent protein (YFP) tagging techniques. Preliminary data indicate a delayed and linear rising of the intensity signal indicating a slow kinetic for the accumulation of DNA repair protein 53BP1. A slow and limited foci diffusion has also been observed. Further investigations are required to assess whatever such diffusion is consistent with a random walk pattern or if it is the result of a more structured lesion processing phenomenon. In conclusion, our data indicates that the use of microbeams coupled to live cell microscopy represent a sophisticated approach for visualizing and quantifying the dynamics changes of DNA proteins at the damaged sites.

Modelling the cycling of persistent organic pollutants (POPs) in the North Sea system: Fluxes, loading, seasonality, trends

The fate and cycling of two selected POPs is investigated for the North Sea system with an improved version of a fate and transport ocean model (FANTOM). The model uses atmospheric data from the EMEP MSC East POP model (Gusev et al., 2009), giving reasonable concentrations and seasonal distributions for the entire region, as opposed to the three observation stations that Ilyina et al. (2006) were limited to. Other model improvements include changes in the calculation of POP exchange between the water column and sediment.

We chose to simulate the fate of two POPs with very different properties, ?-HCH and PCB 153. Since the fate and cycling of POPs are strongly affected by hydrodynamic processes, a high resolution version of the Hamburg Shelf Ocean Model (HAMSOM) was developed and utilised. Simulations were made for the period 1996–2005. Both models were validated by comparing results with available data, which showed that the simulations were of very satisfactory quality.

Model results show that the North Sea is a net sink for ?-HCH and a net source to the atmosphere of PCB 153. Total masses of ?-HCH and PCB 153 in 2005 are reduced to 30% and 50%, respectively, of 1996 values.

Storms resuspending bottom sediments into the water column mobilise POPs into the atmosphere and have the potential to deliver substantial loads of these POPs into Europe.

Degradation of 4-fluorobiphenyl in soil investigated by 19F NMR spectroscopy and 14C radiolabelling analysis

The incubation of the model pollutant [U-14C]'-4-fluorobiphenyl (4FBP) in soil, in the presence and absence of biphenyl (a co-substrate), was carried out in order to study the qualitative disposition and fate of the compound using 14C-HPLC and 19F NMR spectroscopy. Components accounted for using the radiolabel were volatilization, CO2 evolution, organic solvent extractable and bound residue. Quantitative analysis of these data gave a complete mass balance. After sample preparation. 14C-HPLC was used to establish the number of 4FBP related components present in the organic solvent extract. 19F NMR was also used to quantify the organic extracts and to identify the components of the extract. Both approaches showed that the composition of the solvent extractable fractions comprised only parent compound with no metabolites present. As the 14C radiolabel was found to be incorporated into the soil organic matter this indicates that metabolites were being generated, but were highly transitory as incorporation into the SOM was rapid. The inclusion of the co-substrate biphenyl was to increase the overall rate of degradation of 4FBP in soil. The kinetics of disappearance of parent from the soil using the data obtained were investigated from both techniques. This is the first report describing the degradation of a fluorinated biphenyl in soil.

Depletion of the ubiquitin-binding adaptor molecule SQSTM1/p62 from macrophages harboring cftr ΔF508 mutation improves the delivery of Burkholderia cenocepacia to the autophagic machinery

Cystic fibrosis is the most common inherited lethal disease in Caucasians. It is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR), of which the cftr ?F508 mutation is the most common. ?F508 macrophages are intrinsically defective in autophagy because of the sequestration of essential autophagy molecules within unprocessed CFTR aggregates. Defective autophagy allows Burkholderia cenocepacia (B. cepacia) to survive and replicate in ?F508 macrophages. Infection by B. cepacia poses a great risk to cystic fibrosis patients because it causes accelerated lung inflammation and, in some cases, a lethal necrotizing pneumonia. Autophagy is a cell survival mechanism whereby an autophagosome engulfs non-functional organelles and delivers them to the lysosome for degradation. The ubiquitin binding adaptor protein SQSTM1/p62 is required for the delivery of several ubiquitinated cargos to the autophagosome. In WT macrophages, p62 depletion and overexpression lead to increased and decreased bacterial intracellular survival, respectively. In contrast, depletion of p62 in ?F508 macrophages results in decreased bacterial survival, whereas overexpression of p62 leads to increased B. cepacia intracellular growth. Interestingly, the depletion of p62 from ?F508 macrophages results in the release of the autophagy molecule beclin1 (BECN1) from the mutant CFTR aggregates and allows its redistribution and recruitment to the B. cepacia vacuole, mediating the acquisition of the autophagy marker LC3 and bacterial clearance via autophagy. These data demonstrate that p62 differentially dictates the fate of B. cepacia infection in WT and ?F508 macrophages.

Strategies of actin reorganisation in plant cells

Spatial-temporal flexibility of the actin filament network (F-actin) is essential for all basic cellular functions and is governed by a stochastic dynamic model. In this model, actin filaments that randomly polymerise from a pool of free actin are bundled with other filaments and severed by ADF/cofilin. The fate of the severed fragments is not known. It has been proposed that the fragments are disassembled and the monomeric actin recycled for the polymerisation of new filaments. Here, we have generated tobacco cell lines and Arabidopsis plants expressing the actin marker Lifeact to address the mechanisms of F-actin reorganisation in vivo. We found that F-actin is more dynamic in isotropically expanding cells and that the density of the network changes with a periodicity of 70 seconds. The depolymerisation rate, but not the polymerisation rate, of F-actin increases when microtubules are destabilised. New filaments can be assembled from shorter free cytoplasmic fragments, from the products of F-actin severing and by polymerisation from the ends of extant filaments. Thus, remodelling of F-actin might not require bulk depolymerisation of the entire network, but could occur via severing and end-joining of existing polymers.

Recent contribution of sediments and fluids to the mantle's volatile budget

Subduction modifies the cycling of Earth's volatile elements. Fluid-rich sediments and hydrated oceanic lithosphere enter the convecting mantle at subduction zones. Some of the sediments and volatile components are released from the subducting slab, promote mantle melting and are returned to the surface by volcanism. The remainder continue into the deeper mantle. Quantification of the fate of these volatiles requires an understanding of both the nature and timing of fluid release and mantle melting(1). Here we analyse the trace element and isotopic geochemistry of fragments of upper mantle rocks that were transported to the surface by volcanic eruptions above the Batan Island subduction zone, Philippines. We find that the mantle fragments exhibit extreme disequilibrium between their U-Th-Ra isotopic ratios, which we interpret to result from the interaction of wet sediment melts and slab-derived fluids with rocks in the overlying mantle wedge. We infer that wet sediments were delivered from the slab to the mantle wedge between 8,000 and 10,000 years ago, whereas aqueous fluids were delivered separately much later. We estimate that about 625 ppm of water is retained in the wedge. A significant volume of water could therefore be delivered to the mantle transition zone at the base of the upper mantle, or even to the deeper mantle.

Degradation of the polycyclic aromatic hydrocarbon (PAH) fluorene is retarded in a Scots pine ectomycorrhizosphere

Polycyclic aromatic hydrocarbons (PAHs) are an important class of persistent organic pollutants (POPs) in the environment and accumulate in forest soils. These soils are often dominated by ectomycorrhizal (EcM) roots, but little is known about how EcM fungi degrade PAHs, or the overall effect of field colonized EcM roots on the fate of PAHs. The ability of eight EcM fungi to degrade PAHs in liquid culture spiked with ¹⁴C labelled PAHs was investigated. Microcosms were used to determine the impact of naturally colonized mycorrhizal pine seedlings on PAH mineralization and volatilization. Only two EcM fungi (Thelephora terrestris and Laccaria laccata) degraded at least one PAH and none were able to mineralize the PAHs in pure culture. Where degradation occurred, the compounds were only mono-oxygenated. EcM pine seedlings did not alter naphthalene mineralization or volatilization but retarded fluorene mineralization by 35% compared with unplanted, ectomycorrhizosphere soil inoculated, microcosms. The EcM fungi possessed limited PAH degrading abilities, which may explain why EcM dominated microcosms retarded fluorene mineralization. This observation is considered in relation to the 'Gadgil-effect', where retarded litter decomposition has been observed in the presence of EcM roots. © New Phytologist (2004).

Storage of sediment-associated nutrients and contaminants in river channel and floodplain systems

Samples of fine-grained channel bed sediment and overbank floodplain deposits were collected along the main channels of the Rivers Aire (and its main tributary, the River Calder) and Swale, in Yorkshire, UK, in order to investigate downstream changes in the storage and deposition of heavy metals (Cr, Cu, Pb, Zn), total P and the sum of selected PCB congeners, and to estimate the total storage of these contaminants within the main channels and floodplains of these river systems. Downstream trends in the contaminant content of the <63 μm fraction of channel bed and floodplain sediment in the study rivers are controlled mainly by the location of the main sources of the contaminants, which varies between rivers. In the Rivers Aire and Calder, the contaminant content of the <63 μm fraction of channel bed and floodplain sediment generally increases in a downstream direction, reflecting the location of the main urban and industrialized areas in the middle and lower parts of the basin. In the River Swale, the concentrations of most of the contaminants examined are approximately constant along the length of the river, due to the relatively unpolluted nature of this river. However, the Pb and Zn content of fine channel bed sediment decreases downstream, due to the location of historic metal mines in the headwaters of this river, and the effect of downstream dilution with uncontaminated sediment. The magnitude and spatial variation of contaminant storage and deposition on channel beds and floodplains are also controlled by the amount of <63 μm sediment stored on the channel bed and deposited on the floodplain during overbank events. Consequently, contaminant deposition and storage are strongly influenced by the surface area of the floodplain and channel bed. Contaminant storage on the channel beds of the study rivers is, therefore, generally greatest in the middle and lower reaches of the rivers, since channel width increases downstream. Comparisons of the estimates of total storage of specific contaminants on the channel beds of the main channel systems of the study rivers with the annual contaminant flux at the catchment outlets indicate that channel storage represents <3% of the outlet flux and is, therefore, of limited importance in regulating that flux. Similar comparisons between the annual deposition flux of specific contaminants to the floodplains of the study rivers and the annual contaminant flux at the catchment outlet, emphasise the potential importance of floodplain deposition as a conveyance loss. In the case of the River Aire the floodplain deposition flux is equivalent to between ca. 2% (PCBs) and 36% (Pb) of the outlet flux. With the exception of PCBs, for which the value is ≅0, the equivalent values for the River Swale range between 18% (P) and 95% (Pb). The study emphasises that knowledge of the fine-grained sediment delivery system operating in a river basin is an essential prerequisite for understanding the transport and storage of sediment-associated contaminants in river systems and that conveyance losses associated with floodplain deposition exert an important control on downstream contaminant fluxes and the fate of such contaminants. © 2003 Elsevier Science Ltd. All rights reserved.

A novel method of quantifying root exudation in the presence of soil microflora

A microcosm is described in which root exudation may be estimated in the presence of microorganisms. Ryegrass seedlings are grown in microcosms in which roots were spatially separated from a microbial inoculant by a Millipore membrane. Seedlings grown in the microcosms were labelled with [¹⁴C]-CO₂, and the fate of the label within the plant and rhizosphere was determined. Inoculation of the microcosms with Cladosporium resinae increased net fixation of the [¹⁴C] label compared to plants grown under sterile conditions. Inoculation also increased root exudation. The use of the microcosm was illustrated and its applications discussed. © 1991 Kluwer Academic Publishers.