Discovery and Assessment of New Target Sites for Anti-HIV Therapies

Human immunodeficiency virus (HIV) infects cells by endocytosis and takes over parts of the cell’s reaction pathways in order to reproduce itself and spread the infection. One such pathway taken over by HIV becomes the inflammatory pathway which uses Nuclear Factor κB (NF-κB) as the principal transcription factor. Therefore, knocking out the NF-κB pathway would prevent HIV from reproducing itself. In this report, our goal is to produce a simple model for this pathway with which we can identify potential targets for anti-HIV therapies and test out various hypotheses. We present a very simple model with four coupled first-order ODEs and see what happens if we treat IκK concentration as a parameter that can be controlled (by some unspecified means). In Section 3, we augment this model to account for activation and deactivation of IκK, which is controlled (again, by some unspecified means) by TNF

GSUE: urban geochemical mapping in Great Britain

The British Geological Survey is responsible for the national strategic geochemical survey of Great Britain. As part of this programme, the Geochemical Surveys of Urban Environments (GSUE) project was initiated in 1992 and to date, 21 cities have been mapped. Urban sampling is based upon the collection of top (0.05 to 0.20 m) and deeper (0.35 to 0.50 m) soil samples on a 500 m grid across the built environment (1 sample per 0.25 km2). Samples are analysed for c. 46 total element concentrations by X-ray Fluorescence Spectrometry (XRFS), pH and loss on ignition (LOI) as an indicator of organic matter content. The data provide an overview of the urban geochemical signature and because they are collected as part of a national baseline programme, can be readily compared with soils in the rural hinterland to assess the extent of urban contamination. The data are of direct relevance to current UK land use planning, urban regeneration and contaminated land legislative regimes. An overview of the project and applications of the data to human health risk assessment, water quality protection and contaminant source identification are presented

Anomalous enrichment of molybdenum and associated metals in Lower Jurassic (Lias Group) black shales of central England, as revealed by systematic geochemical surveys

Systematic multi-media geochemical surveying by the British Geological Survey's Geochemical Baseline Survey of the Environment (G-BASE) project has revealed significant anomalous patterns of enrichment for a suite of elements – copper (Cu) and uranium (U) – with exceptionally high levels of molybdenum (Mo), in soils and stream sediments in central England. Enrichment of these elements is most often associated with organic-rich, sulphidic ‘black shale’ lithofacies, typical of oxygen-deficient, euxinic depositional environments. The main anomaly lies between Evesham and Rugby where the bedrock comprises the Blue Lias and Charmouth Mudstone formations. Concentrations of Mo are particularly high, reaching soil values of 50 mg/kg, where the regional background is <2 mg/kg. Analysis of black shale partings sampled from rhythmic limestone–shale couplets reveal Mo levels up to 320 mg/kg. Complementary X-ray diffraction analyses suggest that the anomalous Mo levels are hosted by sulphidic (pyrite) rather than organic phases. High Mo levels may have significant impacts on local agriculture, as well as revealing hitherto unsuspected periods of hypoxic and anoxic bottom water sedimentation within localised basins in central England during the Early Jurassic. Rhythmic alternations of thin beds of Mo-rich, sulphidic black shale (euxinic) with bioclastic and micritic limestone (oxic) represent primary depositional cycles rather than a diagenetic origin. The bed-scale cyclicity is attributed to previously described orbitally-induced precession cycles that influenced climate. These resulted in periods of basin anoxia and black shale sedimentation during periods of enhanced terrestrial fresh-water run-off (possibly below a low-salinity pycnocline), alternating with periods of oxygenation of the sea-water and bottom sediments during overturn of the water column

Mathematical models for vulnerable plaques

A plaque is an accumulation and swelling in the artery walls and typically consists of cells, cell debris, lipids, calcium deposits and fibrous connective tissue. A person is likely to have many plaques inside his/her body even if they are healthy. However plaques may become "vulnerable", "high-risk" or "thrombosis-prone" if the person engages in a high-fat diet and does not exercise regularly. In this study group, we proposed two mathematical models to describe plaque growth and rupture. The first model is a mechanical one that approximately treats the plaque as an inflating elastic balloon. In this model, the pressure inside the core increases and then decreases suggesting that plaque stabilization and prevention of rupture is possible. The second model is a biochemical one that focuses on the role of MMPs in degrading the fibrous plaque cap. The cap stress, MMP concentration, plaque volume and cap thickness are coupled together in a system of phenomenological equations. The equations always predict an eventual rupture since the volume, stresses and MMP concentrations generally grow without bound. The main weakness of the model is that many of the important parameters that control the behavior of the plaque are unknown. The two simple models suggested by this group could serve as a springboard for more realistic theoretical studies. But most importantly, we hope they will motivate more experimental work to quantify some of the important mechanical and biochemical properties of vulnerable plaques

Fractionation of lead in soil by isotopic dilution and sequential extraction

‘Reactivity’ or ‘lability’ of lead is difficult to measure using traditional methods. We investigated the use of isotopic dilution with 204Pb to determine metal reactivity in four soils historically contaminated with contrasting sources of Pb, including (i) petrol-derived Pb, (ii) Pb/Zn minespoil, (iii) long-term sewage sludge application and (iv) 19th century urban waste disposal; total soil Pb concentrations ranged from 217 to 13 600 mg kg–1. A post-spike equilibration period of 3 days and suspension in 5.0 × 10–4 M ethylenediaminetetraacetic acid provided reasonably robust conditions for measuring isotopically exchangeable Pb. However, in acidic organic soils a dilute Ca(NO3)2 electrolyte may be preferable to avoid mobilisation of ‘non-labile’ Pb. Results showed that the reactive pool of soil Pb can be a large proportion of the total soil lead content but varies with the original Pb source. A comparison of isotopic exchangeability with the results of a sequential extraction procedure showed that (isotopically) ‘non-labile’ Pb may be broadly equated with ‘residual’ Pb in organic soils. However, in mineral soils the ‘carbonate’ and ‘oxide-bound’ Pb fractions included non-labile forms of Pb. The individual isotopic signatures of labile and non-labile Pb pools suggested that, despite prolonged contact with soil, differences between the lability of the original contaminant and the native soil Pb may remain

Evolution of an elliptical bubble in an accelerating extensional flow

Mathematical models that describe the dynamical behavior of a thin gas bubble embedded in a glass fiber during a fiber drawing process have been discussed and analyzed. The starting point for the mathematical modeling was the equations presented in [1] for a glass fiber with a hole undergoing extensional flow. These equations were reconsidered here with the additional reduction that the hole, i.e. the gas bubble, was thin as compared to the radius of the fiber and of finite extent. The primary model considered was one in which the mass of the gas inside the bubble was fixed. This fixed-mass model involved equations for the axial velocity and fiber radius, and equations for the radius of the bubble and the gas pressure inside the bubble. The model equations assumed that the temperature of the furnace of the drawing tower was known. The governing equations of the bubble are hyperbolic and predict that the bubble cannot extend beyond the limiting characteristics specified by the ends of the initial bubble shape. An analysis of pinch-off was performed, and it was found that pinch-off can occur, depending on the parameters of the model, due to surface tension when the bubble radius is small. In order to determine the evolution of a bubble, a numerical method of solution was presented. The method was used to study the evolution of two different initial bubble shapes, one convex and the other non-convex. Both initial bubble shapes had fore-aft symmetry, and it was found that the bubbles stretched and elongated severely during the drawing process. For the convex shape, fore-aft symmetry was lost in the middle of the drawing process, but the symmetry was re-gained by the end of the drawing tower. A small amount of pinch-off was observed at each end for this case, so that the final bubble length was slightly shorter than its theoretical maximum length. For the non-convex initial shape, pinch-off occurred in the middle of the bubble resulting in two bubbles by the end of the fiber draw. The two bubbles had different final pressures and did not have fore-aft symmetry. An extension of the fixed-mass model was considered in which the gas in the bubble was allowed to diffuse into the surrounding glass. The governing equations for this leaky-mass model were developed and manipulated into a form suitable for a numerical treatment

The Mersey Estuary : sediment geochemistry

This report describes a study of the geochemistry of the Mersey estuary carried out between April 2000 and December 2002. The study was the first in a new programme of surveys of the geochemistry of major British estuaries aimed at enhancing our knowledge and understanding of the distribution of contaminants in estuarine sediments. The report first summarises the physical setting, historical development, geology, hydrography and bathymetry of the Mersey estuary and its catchment. Details of the sampling and analytical programmes are then given followed by a discussion of the sedimentology and geochemistry. The chemistry of the water column and suspended particulate matter have not been studied, the chief concern being with the geochemistry of the surface and near-surface sediments of the Mersey estuary and an examination of their likely sources and present state of contamination

Multiscale modelling of vascular tumour growth in 3D: the roles of domain size & boundary condition

We investigate a three-dimensional multiscale model of vascular tumour growth, which couples blood flow, angiogenesis, vascular remodelling, nutrient/growth factor transport, movement of, and interactions between, normal and tumour cells, and nutrient-dependent cell cycle dynamics within each cell. In particular, we determine how the domain size, aspect ratio and initial vascular network influence the tumour's growth dynamics and its long-time composition. We establish whether it is possible to extrapolate simulation results obtained for small domains to larger ones, by constructing a large simulation domain from a number of identical subdomains, each subsystem initially comprising two parallel parent vessels, with associated cells and diffusible substances. We find that the subsystem is not representative of the full domain and conclude that, for this initial vessel geometry, interactions between adjacent subsystems contribute to the overall growth dynamics. We then show that extrapolation of results from a small subdomain to a larger domain can only be made if the subdomain is sufficiently large and is initialised with a sufficiently complex vascular network. Motivated by these results, we perform simulations to investigate the tumour's response to therapy and show that the probability of tumour elimination in a larger domain can be extrapolated from simulation results on a smaller domain. Finally, we demonstrate how our model may be combined with experimental data, to predict the spatio-temporal evolution of a vascular tumour