Induction of the ferritin gene (ftnA) of Escherichia coli by Fe2+–Fur is mediated by reversal of H-NS silencing and is RyhB independent

FtnA is the major iron-storage protein of Escherichia coli accounting for < or = 50% of total cellular iron. The FtnA gene (ftnA) is induced by iron in an Fe(2+)-Fur-dependent fashion. This effect is reportedly mediated by RyhB, the Fe(2+)-Fur-repressed, small, regulatory RNA. However, results presented here show that ftnA iron induction is independent of RyhB and instead involves direct interaction of Fe(2+)-Fur with an 'extended' Fur binding site (containing five tandem Fur boxes) located upstream (-83) of the ftnA promoter. In addition, H-NS acts as a direct repressor of ftnA transcription by binding at multiple sites (I-VI) within, and upstream of, the ftnA promoter. Fur directly competes with H-NS binding at upstream sites (II-IV) and consequently displaces H-NS from the ftnA promoter (sites V-VI) which in turn leads to derepression of ftnA transcription. It is proposed that H-NS binding within the ftnA promoter is facilitated by H-NS occupation of the upstream sites through H-NS oligomerization-induced DNA looping. Consequently, Fur displacement of H-NS from the upstream sites prevents cooperative H-NS binding at the downstream sites within the promoter, thus allowing access to RNA polymerase. This direct activation of ftnA transcription by Fe(2+)-Fur through H-NS antisilencing represents a new mechanism for iron-induced gene expression.

Cloud statistics and cloud radiative effect for a low-mountain site

In 2007, the Atmospheric Radiation Measurement (ARM) Mobile Facility (AMF) was operated for a nine-month period in the Murg Valley, Black Forest, Germany, in support of the Convective and Orographically-induced Precipitation Study (COPS). The synergy of AMF and COPS partner instrumentation was exploited to derive a set of high-quality thermodynamic and cloud property profiles with 30 s resolution. In total, clouds were present 72% of the time, with multi-layer mixed phase (28.4%) and single-layer water clouds (11.3%) occurring most frequently. A comparison with the Cloudnet sites Chilbolton and Lindenberg for the same time period revealed that the Murg Valley exhibits lower liquid water paths (LWPs; median = 37.5 g m−2) compared to the two sites located in flat terrain. In order to evaluate the derived thermodynamic and cloud property profiles, a radiative closure study was performed with independent surface radiation measurements. In clear sky, average differences between calculated and observed surface fluxes are less than 2% and 4% for the short wave and long wave part, respectively. In cloudy situations, differences between simulated and observed fluxes, particularly in the short wave part, are much larger, but most of these can be related to broken cloud situations. The daytime cloud radiative effect (CRE), i.e. the difference of cloudy and clear-sky net fluxes, has been analysed for the whole nine-month period. For overcast, single-layer water clouds, sensitivity studies revealed that the CRE uncertainty is likewise determined by uncertainties in liquid water content and effective radius. For low LWP clouds, CRE uncertainty is dominated by LWP uncertainty; therefore refined retrievals, such as using infrared and/or higher microwave frequencies, are needed.

Analysis of pottery samples from Bourewa, the earliest known Lapita site in Fiji

We have carried out a thorough mineralogical analysis of 16 pottery samples from the Lapita site of Bourwera in Fiji, using micromorphological techniques with optical and polarising microscopes. While the overall mineralogy of all of the samples is similar the samples clearly divide into two groups, namely those with or without the mineral calcite. Our findings are backed up by chemical analysis using SEM–EDX and FTIR. SEM–EDX shows the clear presence of inclusions of calcite in some of the samples; FTIR shows bands arising from calcite in these samples. The study suggests that it is likely that more than one clay source was used for production of this pottery, but that most of the pottery comes from a single source. This finding is in line with previous studies which suggest some trading of pottery between the Fijian islands but a single source of clay for most of the pottery found at Bouwera. We found no evidence for the destruction of CaCO3 by heating upon production of the pottery in line with the known technology of the Lapita people who produced earthenware pottery but not high temperature ceramics.

Ownership, occupation and risk: a view of the City of London office market

Office returns in the City of London are more volatile than in other UK markets. This volatility may reflect fluctuations in capital flows associated with changing patterns of ownership and the growing linkage between real estate and financial markets in the City. Using current and historical data, patterns of ownership in the City are investigated. They reveal that overseas ownership has grown markedly since 1985, that owners are predominantly FIRE-sector firms and that there are strong links between ownership and occupation. This raises concerns about future volatility and systemic risk in a market strongly influenced by the cyclical behaviour and shocks of the international financial system.

Interactions between the physical soil environment and a horizontal ground coupled heat pump, for a domestic site in the UK

There is currently an increased interest of Government and Industry in the UK, as well as at the European Community level and International Agencies (i.e. Department of Energy, American International Energy Agency), to improve the performance and uptake of Ground Coupled Heat Pumps (GCHP), in order to meet the 2020 renewable energy target. A sound knowledge base is required to help inform the Government Agencies and advisory bodies; detailed site studies providing reliable data for model verification have an important role to play in this. In this study we summarise the effect of heat extraction by a horizontal ground heat exchanger (installed at 1 m depth) on the soil physical environment (between 0 and 1 m depth) for a site in the south of the UK. Our results show that the slinky influences the surrounding soil by significantly decreasing soil temperatures. Furthermore, soil moisture contents were lower for the GCHP soil profile, most likely due to temperature-gradient related soil moisture migration effects and a decreased hydraulic conductivity, the latter as a result of increased viscosity (caused by the lower temperatures for the GCHP soil profile). The effects also caused considerable differences in soil thermal properties. This is the first detailed mechanistic study conducted in the UK with the aim to understand the interactions between the soil, horizontal heat exchangers and the aboveground environment. An increased understanding of these interactions will help to achieve an optimum and sustainable use of the soil heat resources in the future. The results of this study will help to calibrate and verify a simulation model that will provide UK-wide recommendations to improve future GCHP uptake and performance, while safeguarding the soil physical resources.

Predicting metal-binding site residues in low-resolution structural models

The accurate prediction of the biochemical function of a protein is becoming increasingly important, given the unprecedented growth of both structural and sequence databanks. Consequently, computational methods are required to analyse such data in an automated manner to ensure genomes are annotated accurately. Protein structure prediction methods, for example, are capable of generating approximate structural models on a genome-wide scale. However, the detection of functionally important regions in such crude models, as well as structural genomics targets, remains an extremely important problem. The method described in the current study, MetSite, represents a fully automatic approach for the detection of metal-binding residue clusters applicable to protein models of moderate quality. The method involves using sequence profile information in combination with approximate structural data. Several neural network classifiers are shown to be able to distinguish metal sites from non-sites with a mean accuracy of 94.5%. The method was demonstrated to identify metal-binding sites correctly in LiveBench targets where no obvious metal-binding sequence motifs were detectable using InterPro. Accurate detection of metal sites was shown to be feasible for low-resolution predicted structures generated using mGenTHREADER where no side-chain information was available. High-scoring predictions were observed for a recently solved hypothetical protein from Haemophilus influenzae, indicating a putative metal-binding site.

Automatic prediction of functional site regions in low-resolution protein structures

World-wide structural genomics initiatives are rapidly accumulating structures for which limited functional information is available. Additionally, state-of-the art structural prediction programs are now capable of generating at least low resolution structural models of target proteins. Accurate detection and classification of functional sites within both solved and modelled protein structures therefore represents an important challenge. We present a fully automatic site detection method, FuncSite, that uses neural network classifiers to predict the location and type of functionally important sites in protein structures. The method is designed primarily to require only backbone residue positions without the need for specific side-chain atoms to be present. In order to highlight effective site detection in low resolution structural models FuncSite was used to screen model proteins generated using mGenTHREADER on a set of newly released structures. We found effective metal site detection even for moderate quality protein models illustrating the robustness of the method.

On the edge: Southern Levantine Epipalaeolithic–Neolithic chronological succession

The broad picture of the cultural and chronological succession from the Epipalaeolithic to the Neolithic in the southern Levant is generally well understood. However, at a more detailed, local level, many questions remain unanswered. In this paper we examine the archaeological record of cultural developments in southern Jordan and the Negev. Focusing on a series of 14C dates from the early occupation of the PPNA site of WF16, we provide a critical review of dating evidence for the region. This review suggests that while the 14C chronology is ambiguous and problematic there is good evidence for a local historical development from the Harifian variant of the Natufian to the early PPNA, well to the south of any core Mediterranean woodland zone. This stresses the importance of considering developments at local scales of analysis, and that the Neolithic transition occurred within a framework of many interacting sub-regional provinces.