Investigating local relationships between trace elements in soils and cancer data

Medical geology research has recognised a number of potentially toxic elements (PTEs), such as arsenic, cobalt, chromium, copper, nickel, lead, vanadium, uranium and zinc, known to influence human disease by their respective deficiency or toxicity. As the impact of infectious diseases has decreased and the population ages, so cancer has become the most common cause of death in developed countries including Northern Ireland. This research explores the relationship between environmental exposure to potentially toxic elements in soil and cancer disease data across Northern Ireland. The incidence of twelve different cancer types (lung, stomach, leukaemia, oesophagus, colorectal, bladder, kidney, breast, mesothelioma, melanoma and non melanoma(NM) both basal and squamous, were examined in the form of twenty-five coded datasets comprising aggregates over the 12 year period from 1993 to 2006. A local modelling technique,geographically weighted regression (GWR) is usedto explore the relationship between environmental exposure and cancer disease data. The results show comparisons of the geographical incidence of certain cancers (stomach and NM squamous skin cancer) in relation to concentrations of certain PTEs (arsenic levels in soils and radon were identified). Findings from the research have implications for regional human health risk assessments.

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.

Pathogenic Yersinia enterocolitica strains increase the outer membrane permeability in response to environmental stimuli by modulating lipopolysaccharide fluidity and lipid A structure

Pathogenic biotypes of Yersinia enterocolitica (serotypes O:3, O:8, O:9, and O:13), but not environmental biotypes (serotypes O:5, O:6, O:7,8, and O:7,8,13,19), increased their permeability to hydrophobic probes when they were grown at pH 5.5 or in EGTA-supplemented (Ca(2+)-restricted) media at 37 degrees C. A similar observation was also made when representative strains of serotypes O:8 and O:5 were tested after brief contact with human monocytes. The increase in permeability was independent of the virulence plasmid. The role of lipopolysaccharide (LPS) in this phenomenon was examined by using Y. enterocolitica serotype O:8. LPS aggregates of bacteria grown in acidic or EGTA-supplemented broth took up more N-phenylnaphthylamine than LPS aggregates of bacteria grown in standard broth and also showed a marked increase in acyl chain fluidity which correlated with permeability, as determined by measurements obtained in the presence of hydrophobic dyes. No significant changes in O-antigen polymerization were observed, but lipid A acylation changed depending on the growth conditions. In standard medium at 37 degrees C, there were hexa-, penta-, and tetraacyl lipid A forms, and the pentaacyl form was dominant. The amount of tetraacyl lipid A increased in EGTA-supplemented and acidic media, and hexaacyl lipid A almost disappeared under the latter conditions. Our results suggest that pathogenic Y. enterocolitica strains modulate lipid A acylation coordinately with expression of virulence proteins, thus reducing LPS packing and increasing outer membrane permeability. The changes in permeability, LPS acyl chain fluidity, and lipid A acylation in pathogenic Y. enterocolitica strains approximate the characteristics in Yersinia pseudotuberculosis and Yersinia pestis and suggest that there is a common outer membrane pattern associated with pathogenicity.

Brucella abortus and its closest phylogenetic relative, Ochrobactrum spp., differ in outer membrane permeability and cationic peptide resistance

The outer membrane (OM) of the intracellular parasite Brucella abortus is permeable to hydrophobic probes and resistant to destabilization by polycationic peptides and EDTA. The significance of these unusual properties was investigated in a comparative study with the opportunistic pathogens of the genus Ochrobactrum, the closest known Brucella relative. Ochrobactrum spp. OMs were impermeable to hydrophobic probes and sensitive to polymyxin B but resistant to EDTA. These properties were traced to lipopolysaccharide (LPS) because (i) insertion of B. abortus LPS, but not of Escherichia coli LPS, into Ochrobactrum OM increased its permeability; (ii) permeability and polymyxin B binding measured with LPS aggregates paralleled the results with live bacteria; and (iii) the predicted intermediate results were obtained with B. abortus-Ochrobactrum anthropi and E. coli-O. anthropi LPS hybrid aggregates. Although Ochrobactrum was sensitive to polymyxin, self-promoted uptake and bacterial lysis occurred without OM morphological changes, suggesting an unusual OM structural rigidity. Ochrobactrum and B. abortus LPSs showed no differences in phosphate, qualitative fatty acid composition, or acyl chain fluidity. However, Ochrobactrum LPS, but not B. abortus LPS, contained galacturonic acid. B. abortus and Ochrobactrum smooth LPS aggregates had similar size and zeta potential (-12 to -15 mV). Upon saturation with polymyxin, zeta potential became positive (1 mV) for Ochrobactrum smooth LPS while remaining negative (-5 mV) for B. abortus smooth LPS, suggesting hindered access to inner targets. These results show that although Ochrobactrum and Brucella share a basic OM pattern, subtle modifications in LPS core cause markedly different OM properties, possibly reflecting the adaptive evolution of B. abortus to pathogenicity.

Yersinia pseudotuberculosis and Yersinia pestis show increased outer membrane permeability to hydrophobic agents which correlates with lipopolysaccharide acyl-chain fluidity

The hydrophobic probe N-phenyl-1-naphthylamine accumulated less in non-pathogenic Yersinia spp. and non-pathogenic and pathogenic Yersinia enterocolitica than in Yersinia pseudotuberculosis or Yersinia pestis. This was largely due to differences in the activity of efflux systems, but also to differences in outer membrane permeability because uptake of the probe in KCN/arsenate-poisoned cells was slower in the former group than in Y. pseudotuberculosis and Y. pestis. The probe accumulation rate was higher in Y. pseudotuberculosis and Y. pestis grown at 37 degrees C than at 26 degrees C and was always highest in Y. pestis. These yersiniae had LPSs with shorter polysaccharides than Y. enterocolitica, particularly when grown at 37 degrees C. Gelliquid-crystalline phase transitions (Tc 28-31 degrees C) were observed in LPS aggregates of Y. enterocolitica grown at 26 and 37 degrees C, with no differences between non-pathogenic and pathogenic strains. Y. pseudotuberculosis and Y. pestis LPSs showed no phase transitions and, although the fluidity of LPSs of Y. pseudotuberculosis and Y. enterocolitica grown at 26 degrees C were close below the Tc of the latter, they were always in a more fluid state than Y. enterocolitica LPS. Comparison with previous studies of Salmonella choleraesuis subsp. choleraesuis serotype minnesota rough LPS showed that the increased fluidity and absence of transition of Y. pseudotuberculosis and Y. pestis LPSs cannot be explained by their shorter polysaccharides and suggested differences at the lipid A/core level. It is proposed that differences in LPS-LPS interactions and efflux activity explain the above observations and reflect the adaptation of Yersinia spp. to different habitats.

Yersinia pseudotuberculosis and Yersinia pestis are more resistant to bactericidal cationic peptides than Yersinia enterocolitica

The action of bactericidal polycationic peptides was compared in Yersinia spp. by testing peptide binding to live cells and changes in outer membrane (OM) morphology and permeability. Moreover, polycation interaction with LPS was studied by measuring the dependence of dansylcadaverine displacement and zeta potential on polycation concentration. When growth at 37 degrees C, Yersinia pestis and Yersinia pseudotuberculosis bound less polymyxin B (PMB) than pathogenic or non-pathogenic Yersinia enterocolitica, regardless of virulence plasmid expression. Y. pseudotuberculosis OMs were unharmed by PMB concentrations causing extensive OM blebbing in Y. enterocolitica. The permeability to lysozyme caused by PMB was greater in Y. enterocolitica than in Y. pseudotuberculosis or Y. pestis and differences increased at 37 degrees C. Similar observations were made with other polycations using a polymyxin/novobiocin permeability assay. With LPS of cells grown at 26 degrees C, polycation binding was highest for Y. pseudotuberculosis and lowest for Y. pestis, with Y. enterocolitica yielding intermediate results which were lower for pathogenic than for non-pathogenic strains. With LPS of cells grown at 37 degrees C, polycation binding remained unchanged for Y. pestis and pathogenic Y. enterocolitica, increased for non-pathogenic Y. enterocolitica and decreased for Y. pseudotuberculosis to Y. pestis levels. Polycation binding related in part to differences in charge density (zeta potential) of LPS aggregates, suggesting similar effects at bacterial surfaces. It is suggested that species and temperature differences in polycation resistance relate to infection route, invasiveness and intracellular multiplication of Yersinia spp.

Influence of the type of coarse lightweight aggregate on properties of Semi-Lightweight Self-Consolidating Concrete

This paper presents studies on the properties of fresh and hardened semilightweight self-consolidating concrete (SLWSCC) mixtures, produced with two types of manufactured coarse lightweight aggregates (LWA) and normal weight sand. The first type, a sintered pulverized fuel ash, was made from an industrial by-product, fly ash, whereas the second one, an expanded clay, was produced from a naturally sourced clay. For all mixtures, normal weight sand was used as a fine fraction of aggregates, and the portland cement was partially replaced with a limestone powder. The SLWSCC was produced with different water presaturation regimes of the LWAs. The desired initial slump-flow spread was set between 700 and 800 mm. The effect of three superplasticizers was evaluated by testing properties of SLWSCC, normal weight SCC, and paste mixtures. Three SCC fresh properties were measured: the slump-flow, the V-funnel flow time, and the J-ring blocking step. Moreover, the slump-flow loss was evaluated. The degree of segregation was assessed in both fresh and hardened states. Additionally, the hardened density and the compressive strengths were tested. All SLWSCC mixtures were produced with a desired range of slump-flow spread and with satisfactory passing ability assessed with the J-ring test. SLWSCCs prepared with the expanded clay LWA were less sensitive to the variation of water presaturation levels and showed lower viscosity than those made with the sintered pulverized fuel ash LWA. Only mixtures containing SP-3 superplasticizer showed acceptable workability loss resistance. The saturated surface-dry density of all of the mixtures varied in a range of 2,025–2,125??kg/m 3 . Mixtures containing 29% of coarse LWAs and 71% of sand (by mass) had 24-h and 28-day compressive strengths above 20 and 40 MPa, respectively, but the mixtures made with the expanded clay were slightly weaker.

Precise Subnanometer Plasmonic Junctions for SERS within Gold Nanoparticle Assemblies Using Cucurbit[n]uril "Glue"

Cucurbit[n]urils (CB[n]) are macrocyclic host molecules with subnanometer dimensions capable of binding to gold surfaces. Aggregation of gold nanoparticles with CB[n] produces a repeatable, fixed, and rigid interparticle separation of 0.9 nm, and thus such assemblies possess distinct and exquisitely sensitive plasmonics. Understanding the plasmonic evolution is key to their use as powerful SERS substrates. Furthermore, this unique spatial control permits fast nanoscale probing of the plasmonics of the aggregates "glued" together by CBs within different kinetic regimes using simultaneous extinction and SERS measurements. The kinetic rates determine the topology of the aggregates including the constituent structural motifs and allow the identification of discrete plasmon modes which are attributed to disordered chains of increasing lengths by theoretical simulations. The CBs directly report the near-field strength of the nanojunctions they create via their own SERS, allowing calibration of the enhancement. Owing to the unique barrel-shaped geometry of CB[n] and their ability to bind "guest" molecules, the aggregates afford a new type of in situ self-calibrated and reliable SERS substrate where molecules can be selectively trapped by the CB[n] and exposed to the nanojunction plasmonic field. Using this concept, a powerful molecular-recognition-based SERS assay is demonstrated by selective cucurbit[n]uril host-guest complexation.

Translation suppression promotes stress granule formation and cell survival in response to cold shock

Cells respond to different types of stress by inhibition of protein synthesis and subsequent assembly of stress granules (SGs), cytoplasmic aggregates that contain stalled translation preinitiation complexes. Global translation is regulated through the translation initiation factor eukaryotic initiation factor 2a (eIF2a) and the mTOR pathway. Here we identify cold shock as a novel trigger of SG assembly in yeast and mammals. Whereas cold shock-induced SGs take hours to form, they dissolve within minutes when cells are returned to optimal growth temperatures. Cold shock causes eIF2a phosphorylation through the kinase PERK in mammalian cells, yet this pathway is not alone responsible for translation arrest and SG formation. In addition, cold shock leads to reduced mitochondrial function, energy depletion, concomitant activation of AMP-activated protein kinase (AMPK), and inhibition of mTOR signaling. Compound C, a pharmacological inhibitor of AMPK, prevents the formation of SGs and strongly reduces cellular survival in a translation-dependent manner. Our results demonstrate that cells actively suppress protein synthesis by parallel pathways, which induce SG formation and ensure cellular survival during hypothermia.

Dynamic oscillation of translation and stress granule formation mark the cellular response to virus infection

Virus infection-induced global protein synthesis suppression is linked to assembly of stress granules (SGs), cytosolic aggregates of stalled translation preinitiation complexes. To study long-term stress responses, we developed an imaging approach for extended observation and analysis of SG dynamics during persistent hepatitis C virus (HCV) infection. In combination with type 1 interferon, HCV infection induces highly dynamic assembly/disassembly of cytoplasmic SGs, concomitant with phases of active and stalled translation, delayed cell division, and prolonged cell survival. Double-stranded RNA (dsRNA), independent of viral replication, is sufficient to trigger these oscillations. Translation initiation factor eIF2a phosphorylation by protein kinase R mediates SG formation and translation arrest. This is antagonized by the upregulation of GADD34, the regulatory subunit of protein phosphatase 1 dephosphorylating eIF2a. Stress response oscillation is a general mechanism to prevent long-lasting translation repression and a conserved host cell reaction to multiple RNA viruses, which HCV may exploit to establish persistence.

Exploring the free energy surfaces of clusters using reconnaissance metadynamics

A new approach is proposed for exploring the low-energy structures of small to medium-sized aggregates of atoms and molecules. This approach uses the recently proposed reconnaissance metadynamics method [G. A. Tribello, M. Ceriotti, and M. Parrinello. Proc. Natl. Acad. Sci. U.S.A. 107(41), 17509 (2010)] in tandem with collective variables that describe the average structure of the coordination sphere around the atoms/molecules. We demonstrate this method on both Lennard-Jones and water clusters and show how it is able to quickly find the global minimum in the potential energy surface, while exploring the finite temperature free energy surface. (C) 2011 American Institute of Physics. [doi: 10.1063/1.3628676]

On thin ice: surface order and disorder during pre-melting

The effect of temperature on the structure of the ice Ih (0001) surface is considered through a series of molecular dynamics simulations on an ice slab. At relatively low temperatures (200K) a small fraction of surface self-interstitials (i.e. admolecules) appear that are formed exclusively from molecules leaving the outermost bilayer. At higher temperatures (ca. 250 K), vacancies start to appear in the inner part of the outermost bilayer exposing the underlying bilayer and providing sites with a high concentration of the dangling hydrogen bonds. Around 250-260 K aggregates of molecules formed on top of the outermost bilayer from self-interstitials become more mobile and have diffusivities approaching that of liquid water. At similar to 270-280 K the inner bilayer of one surface noticeably destructures and it appears that at above 285 K both surfaces are melting. The observed disparity in the onset of melting between the two sides of the slab is rationalised by considering the relationship between surface energy and the spatial distribution of protons at the surface; thermodynamic stability is conferred on the surface by maximising separations between dangling protons at the crystal exterior. Local hotspots associated with a high dangling proton density are suggested to be susceptible to pre-melting and may be more efficient at trapping species at the external surface than regions with low concentrations of protons thus potentially helping ice particles to catalyse reactions. A preliminary conclusion of this work is that only about 10-20 K below the melting temperature of the particular water potential employed is major disruption of the crystalline lattice noted which could be interpreted as being "liquid", the thickness of this film being about a nanometre.

Arbuscular mycorrhizal fungi and collembola non-additively increase soil aggregation

Soil aggregation is a principal ecosystem process mediated by soil biota. Collembola and arbuscular mycorrhizal (AM) fungi are important groups in the soil, and can interact in various ways. Few studies have examined collembola effects on soil aggregation, while many have quantified AM effects. Here, we asked if collembola have any effect on soil aggregation, and if they alter AM fungi-mediated effects on soil aggregation.

We carried out a factorial greenhouse study, manipulating the presence of both collembola and AM fungi, using two different plant species, Sorghum vulgare and Daucus carota. We measured root length and biomass, AMF (and non-AMF) soil hyphal length, root colonization, and collembolan populations, and quantified water stable soil aggregates (WSA) in four size classes.

Soil exposed to growth of AMF hyphae and collembola individually had higher WSA than control treatments. Moreover, the interaction effects between AMF and collembola were significant, with nonadditive increases in the combined application compared to the single treatments.

Our findings show that collembola can play a crucial role in maintaining ecological sustainability through promoting soil aggregation, and point to the importance of considering organism interactions in understanding formation of soil structure. (C) 2011 Elsevier Ltd. All rights reserved.

Direct, positive feedbacks produce instability in models of interrelationships among soil structure, plants and arbuscular mycorrhizal fungi

Current conceptual models of reciprocal interactions linking soil structure, plants and arbuscular mycorrhizal fungi emphasise positive feedbacks among the components of the system. However, dynamical systems with high dimensionality and several positive feedbacks (i.e. mutualism) are prone to instability. Further, organisms such as arbuscular mycorrhizal fungi (AMF) are obligate biotrophs of plants and are considered major biological agents in soil aggregate stabilization. With these considerations in mind, we developed dynamical models of soil ecosystems that reflect the main features of current conceptual models and empirical data, especially positive feedbacks and linear interactions among plants, AMF and the component of soil structure dependent on aggregates. We found that systems become increasingly unstable the more positive effects with Type I functional response (i.e., the growth rate of a mutualist is modified by the density of its partner through linear proportionality) are added to the model, to the point that increasing the realism of models by adding linear effects produces the most unstable systems. The present theoretical analysis thus offers a framework for modelling and suggests new directions for experimental studies on the interrelationship between soil structure, plants and AMF. Non-linearity in functional responses, spatial and temporal heterogeneity, and indirect effects can be invoked on a theoretical basis and experimentally tested in laboratory and field experiments in order to account for and buffer the local instability of the simplest of current scenarios. This first model presented here may generate interest in more explicitly representing the role of biota in soil physical structure, a phenomenon that is typically viewed in a more process- and management-focused context. (C) 2011 Elsevier Ltd. All rights reserved.

Are power laws that estimate fractal dimension a good descriptor of soil structure and its link to soil biological properties?

The study of interrelationships between soil structure and its functional properties is complicated by the fact that the quantitative description of soil structure is challenging. Soil scientists have tackled this challenge by taking advantage of approaches such as fractal geometry, which describes soil architectural complexity through a scaling exponent (D) relating mass and numbers of particles/aggregates to particle/aggregate size. Typically, soil biologists use empirical indices such as mean weight diameters (MWD) and percent of water stable aggregates (WSA), or the entire size distribution, and they have successfully related these indices to key soil features such as C and N dynamics and biological promoters of soil structure. Here, we focused on D, WSA and MWD and we tested whether: D estimated by the exponent of the power law of number-size distributions is a good and consistent correlate of MWD and WSA; D carries information that differs from MWD and WSA; the fraction of variation in D that is uncorrelated with MWD and WSA is related to soil chemical and biological properties that are thought to establish interdependence with soil structure (e.g., organic C, N, arbuscular mycorrhizal fungi). We analysed observational data from a broad scale field study and results from a greenhouse experiment where arbuscular mycorrhizal fungi (AMF) and collembola altered soil structure. We were able to develop empirical models that account for a highly significant and large portion of the correlation observed between WSA and MWD but we did not uncover the mechanisms that underlie this correlation. We conclude that most of the covariance between D and soil biotic (AMF, plant roots) and abiotic (C. N) properties can be accounted for by WSA and MWD. This result implies that the ecological effects of the fragmentation properties described by D and generally discussed under the framework of fractal models can be interpreted under the intuitive perspective of simpler indices and we suggest that the biotic components mostly impacted the largest size fractions, which dominate MWD, WSA and the scaling exponent ruling number-size distributions. (C) 2010 Elsevier Ltd. All rights reserved.