Elucidation of the Burkholderia cenocepacia hopanoid biosynthesis pathway uncovers functions for conserved proteins in hopanoid-producing bacteria

Hopanoids are bacterial surrogates of eukaryotic membrane sterols and among earth's most abundant natural products. Their molecular fossils remain in sediments spanning more than a billion years. However, hopanoid metabolism and function are not fully understood. Burkholderia species are environmental opportunistic pathogens that produce hopanoids and also occupy diverse ecological niches. We investigated hopanoids biosynthesis in Burkholderia cenocepacia by deletion mutagenesis and structural characterization of the hopanoids produced by the mutants. The enzymes encoded by hpnH and hpnG were essential for production of all C35 extended hopanoids, including bacteriohopanetetrol (BHT), BHT glucosamine and BHT cyclitol ether. Deletion of hpnI resulted in BHT production, while ΔhpnJ produced only BHT glucosamine. Thus, HpnI is required for BHT glucosamine production while HpnJ is responsible for its conversion to the cyclitol ether. The ΔhpnH and ΔhpnG mutants could not grow under any stress condition tested, whereas ΔhpnI, ΔhpnJ and ΔhpnK displayed wild-type growth rates when exposed to detergent, but varying levels of sensitivity to low pH and polymyxin B. This study not only elucidates the biosynthetic pathway of hopanoids in B. cenocepacia, but also uncovers a biosynthetic role for the conserved proteins HpnI, HpnJ and HpnK in other hopanoid-producing bacteria.whereas ΔhpnI, ΔhpnJ and ΔhpnK displayed wild-type growth rates when exposed to detergent, but varying levels of sensitivity to low pH and polymyxin B. This study not only elucidates the biosynthetic pathway of hopanoids in B. cenocepacia, but also uncovers a biosynthetic role for the conserved proteins HpnI, HpnJ and HpnK in other hopanoid-producing bacteria.

Estimating male and female height inequality

This study investigates the coefficient of variation (CV) of height of males and females as a measure of inequality. We have collected a data set on corresponding male and female height CVs from 124 populations, spanning the period between the 1840s and 1980s. The results suggest that the R2 between the two CVs is 0.39, with the male CV being greater, indicating higher plasticity.

Biological insights from 108 schizophrenia-associated genetic loci

Schizophrenia is a highly heritable disorder. Genetic risk is conferred by a large number of alleles, including common alleles of small effect that might be detected by genome-wide association studies. Here we report a multi-stage schizophrenia genome-wide association study of up to 36,989 cases and 113,075 controls. We identify 128 independent associations spanning 108 conservatively defined loci that meet genome-wide significance, 83 of which have not been previously reported. Associations were enriched among genes expressed in brain, providing biological plausibility for the findings. Many findings have the potential to provide entirely new insights into aetiology, but associations at DRD2 and several genes involved in glutamatergic neurotransmission highlight molecules of known and potential therapeutic relevance to schizophrenia, and are consistent with leading pathophysiological hypotheses. Independent of genes expressed in brain, associations were enriched among genes expressed in tissues that have important roles in immunity, providing support for the speculated link between the immune system and schizophrenia.

Direct Detection of YORP Spin-up on Asteroid (25143) Itokawa and Implications for its Internal Structure

Near-Earth asteroid (25143) Itokawa was visited by the Hayabusa spacecraft in 2005, resulting in a highly detailed surface shape and topography model. This model has led to several predictions for the expected radiative torques on this asteroid, suggesting that its spin rate should be decelerating. Through an observational survey spanning 2001 to 2013 we have successfully measured an acceleration in its spin rate of dω/dt = 3.54 (± 0.38) × 10^(-8) rad day^(-2), equivalent to a decrease of its rotation period of ~ 45 ms year^(-1). Using the shape model determined from the Hayabusa spacecraft, we applied a detailed thermophysical analysis, to reconcile the predicted YORP strength with that observed. We find that the center-of-mass for Itokawa must be shifted by ~20 m along the long-axis of the asteroid to reconcile observations with theory. This can be explained if Itokawa is composed of two separate bodies with very different bulk densities of 1740 ± 110 kg m^(-3) and 2730 ± 440 kg m^(-3), and was formed from the merger of two separate bodies, consistent with the collapse of a binary system or the re-accumulation of material from a catastrophic collisional disruption. We demonstrate that an observational measurement of radiative torques, when combined with a detailed shape model, can provide insight into the interior structure of an asteroid.

Low-Power Process-Variation Tolerant Arithmetic Units Using Input-Based Elastic Clocking

In this paper we propose a design methodology for low-power high-performance, process-variation tolerant architecture for arithmetic units. The novelty of our approach lies in the fact that possible delay failures due to process variations and/or voltage scaling are predicted in advance and addressed by employing an elastic clocking technique. The prediction mechanism exploits the dependence of delay of arithmetic units upon input data patterns and identifies specific inputs that activate the critical path. Under iso-yield conditions, the proposed design operates at a lower scaled down Vdd without any performance degradation, while it ensures a superlative yield under a design style employing nominal supply and transistor threshold voltage. Simulation results show power savings of upto 29%, energy per computation savings of upto 25.5% and yield enhancement of upto 11.1% compared to the conventional adders and multipliers implemented in the 70nm BPTM technology. We incorporated the proposed modules in the execution unit of a five stage DLX pipeline to measure performance using SPEC2000 benchmarks [9]. Maximum area and throughput penalty obtained were 10% and 3% respectively.

Software as a Service: Analysing Security Issues

Software-as-a-service (SaaS) is a type of software service delivery model which encompasses a broad range of business opportunities and challenges. Users and service providers are reluctant to integrate their business into SaaS due to its security concerns while at the same time they are attracted by its benefits. This article highlights SaaS utility and applicability in different environments like cloud computing, mobile cloud computing, software defined networking and Internet of things. It then embarks on the analysis of SaaS security challenges spanning across data security, application security and SaaS deployment security. A detailed review of the existing mainstream solutions to tackle the respective security issues mapping into different SaaS security challenges is presented. Finally, possible solutions or techniques which can be applied in tandem are presented for a secure SaaS platform.

Distal Deposition of Tephra from the Eyjafjallajökull 2010 Summit Eruption

The 2010 Eyjafjallajökull lasted 39 days and had 4 different phases, of which the first and third (14–18 April and 5–6 May) were most intense. Most of this period was dominated by winds with a northerly component that carried tephra toward Europe, where it was deposited in a number of locations and was sampled by rain gauges or buckets, surface swabs, sticky-tape samples and air filtering. In the UK, tephra was collected from each of the Phases 1–3 with a combined range of latitudes spanning the length of the country. The modal grain size of tephra in the rain gauge samples was 25 um, but the largest grains were 100 um in diameter and highly vesicular. The mass loading was equivalent to 8–218 shards cm2, which is comparable to tephra layers from much larger past eruptions. Falling tephra was collected on sticky tape in the English Midlands on 19, 20 and 21st April (Phase 2), and was dominated by aggregate clasts (mean diameter 85 um, component grains <10 um). SEM-EDS spectra for aggregate grains contained an extra peak for sulphur, when compared to control samples from the volcano, indicating that they were cemented by sulphur-rich minerals e.g. gypsum (CaSO4⋅H2O). Air quality monitoring stations did not record fluctuations in hourly PM10 concentrations outside the normal range of variability during the eruption, but there was a small increase in 24-hour running mean concentration from 21–24 April (Phase 2). Deposition of tephra from Phase 2 in the UK indicates that transport of tephra from Iceland is possible even for small eruption plumes given suitable wind conditions. The presence of relatively coarse grains adds uncertainty to concentration estimates from air quality sensors, which are most sensitive to grain sizes <10 um. Elsewhere, tephra was collected from roofs and vehicles in the Faroe Islands (mean grain size 40 um, but 100 um common), from rainwater in Bergen in Norway (23–91 um) and in air filters in Budapest, Hungary (2–6 um). A map is presented summarizing these and other recently published examples of distal tephra deposition from the Eyjafjallajökull eruption. It demonstrates that most tephra deposited on mainland Europe was produced in the highly explosive Phase 1 and was carried there in 2–3 days.

New age estimates and climatostratigraphic correlations for the Borrobol and Penifiler Tephras: evidence from Abernethy Forest, Scotland

The emerging tephrostratigraphy of NW Europe spanning the last termination (ca. 15–9 ka) provides the potential for synchronizing marine, ice-core and terrestrial records, but is currently compromised by stratigraphic complications, geochemical ambiguity and imprecise age estimates for some layers. Here we present new tephrostratigraphic, radiocarbon and chironomid-based
palaeotemperature data from Abernethy Forest, Scotland, that refine the ages and stratigraphic positions of the Borrobol and Penifiler tephras. The Borrobol Tephra (14.14–13.95 cal ka BP) was deposited in a relatively warm period equated with Greenland Interstadial sub-stage GI-1e. The younger Penifiler Tephra (14.09–13.65 cal ka BP) is closely associated with a cold oscillation equated with GI-
1d. We also present evidence for a previously undescribed tephra layer that has a major-element chemical signature identical to the Vedde Ash. It is associated with the warming trend at the end of the Younger Dryas, and dates between 11.79 and 11.20 cal ka BP.

Systolic two-port adaptor for high performance wave digital filtering

The authors present a VLSI circuit for implementing wave digital filter (WDF) two-port adaptors. Considerable speedups over conventional designs have been obtained using fine grained pipelining. This has been achieved through the use of most significant bit (MSB) first carry-save arithmetic, which allows systems to be designed in which latency L is small and independent of either coefficient or input data wordlength. L is determined by the online delay associated with the computation required at each node in the circuit (in this case a multiply/add plus two separate additions). This in turn means that pipelining can be used to considerably enhance the sampling rate of a recursive digital filter. The level of pipelining which will offer enhancement is determined by L and is fine-grained rather than bit level. In the case of the circuit considered, L = 3. For this reason pipeline delays (half latches) have been introduced between every two rows of cells to produce a system with a once every cycle sample rate.

The latest LGM culmination of the Garda Glacier (Italian Alps) and the onset of glacial termination. Age of glacial collapse and vegetation chronosequence

In the deglacial sequence of the largest end moraine system of the Italian Alps, we focused on the latest culmination of the Last Glacial Maximum, before a sudden downwasting of the piedmontane lobe occupying the modern lake basin. We obtained a robust chronology for this culmination and for the subsequent deglacial history by cross-radiocarbon dating of a proximal fluvioglacial plain and of a deglacial continuous lake sedimentation. We used reworked dinocysts to locate sources of glacial abrasion and to mark the input of glacial meltwater until depletion. The palynological record from postglacial lake sediments provided the first vegetation chronosequence directly reacting to the early Lateglacial withdrawal so far documented in the Alps.

Glacier collapse occurred soon after 17.46 +/- 0.2 ka cal BP, which is, the Manerba advance culmination. Basin deglaciation of several overdeepened foreland piedmont lakes on southern and northern sides of the Alps appears to be synchronous at millennial scale and near-synchronous with large-scale glacial retreat at global scale. The pioneering succession shows a first afforestation step at a median modeled age of 64 years after deglaciation, while rapid tree growth lagged 7 centuries. Between 16.4 +/- 0.16 and 15.5 +/- 0.16 ka cal BP, a regressive phase interrupted forest growth marking a Lateglacial phase of continental-dry climate predating GI-1. This event, spanning the most advanced phases of North-Atlantic H1, is consistently radiocarbon-framed at three deglacial lake records so far investigated on the Italian side of the Alps. Relationships with the Gschnitz stadial from the Alpine record of Lateglacial advances are discussed

Sea-level changes in Iceland and the influence of the North Atlantic Oscillation during the last half millennium

We present a new, diatom-based sea-level reconstruction for Iceland spanning the last -500 years, and investigate the possible mechanisms driving the sea-level changes. A sea-level reconstruction from near the Icelandic low pressure system is important as it can improve understanding of ocean-atmosphere forcing on North Atlantic sea-level variability over multi-decadal to centennial timescales. Our reconstruction is from Viarhólmi salt marsh in Snæfellsnes in western Iceland, a site from where we previously obtained a 2000-yr record based upon less precise sea-level indicators (salt-marsh foraminifera). The 20th century part of our record is corroborated by tide-gauge data from Reykjavik. Overall, the new reconstruction shows ca0.6m rise of relative sea level during the last four centuries, of which ca0.2m occurred during the 20th century. Low-amplitude and high-frequency sea-level variability is super-imposed on the pre-industrial long-term rising trend of 0.65m per 1000 years. Most of the relative sea-level rise occurred in three distinct periods: AD 1620-1650, AD 1780-1850 and AD 1950-2000, with maximum rates of ~3±2mm/yr during the latter two of these periods. Maximum rates were achieved at the end of large shifts (from negative to positive) of the winter North Atlantic Oscillation (NAO) Index as reconstructed from proxy data. Instrumental data demonstrate that a strong and sustained positive NAO (a deep Icelandic Low) generates setup on the west coast of Iceland resulting in rising sea levels. There is no strong evidence that the periods of rapid sea-level rise were caused by ocean mass changes, glacial isostatic adjustment or regional steric change. We suggest that wind forcing plays an important role in causing regional-scale coastal sea-level variability in the North Atlantic, not only on (multi-)annual timescales, but also on multi-decadal to centennial timescales.

Sediment accumulation rates in subarctic lakes: insights into age-depth modeling from 22 dated lake records from the Northwest Territories, Canada

Age-depth modeling using Bayesian statistics requires well-informed prior information about the behavior of sediment accumulation. Here we present average sediment accumulation rates (represented as deposition times, DT, in yr/cm) for lakes in an Arctic setting, and we examine the variability across space (intra- and inter-lake) and time (late Holocene). The dataset includes over 100 radiocarbon dates, primarily on bulk sediment, from 22 sediment cores obtained from 18 lakes spanning the boreal to tundra ecotone gradients in subarctic Canada. There are four to twenty-five radiocarbon dates per core, depending on the length and character of the sediment records. Deposition times were calculated at 100-year intervals from age-depth models constructed using the ‘classical’ age-depth modeling software Clam. Lakes in boreal settings have the most rapid accumulation (mean DT 20 ± 10 years), whereas lakes in tundra settings accumulate at moderate (mean DT 70 ± 10 years) to very slow rates, (>100 yr/cm). Many of the age-depth models demonstrate fluctuations in accumulation that coincide with lake evolution and post-glacial climate change. Ten of our sediment cores yielded sediments as old as c. 9,000 cal BP (BP = years before AD 1950). From between c. 9,000 cal BP and c. 6,000 cal BP, sediment accumulation was relatively rapid (DT of 20 to 60 yr/cm). Accumulation slowed between c. 5,500 and c. 4,000 cal BP as vegetation expanded northward in response to warming. A short period of rapid accumulation occurred near 1,200 cal BP at three lakes. Our research will help inform priors in Bayesian age modeling.

Digital pathology and image analysis in tissue biomarker research

Digital pathology and the adoption of image analysis have grown rapidly in the last few years. This is largely due to the implementation of whole slide scanning, advances in software and computer processing capacity and the increasing importance of tissue-based research for biomarker discovery and stratified medicine. This review sets out the key application areas for digital pathology and image analysis, with a particular focus on research and biomarker discovery. A variety of image analysis applications are reviewed including nuclear morphometry and tissue architecture analysis, but with emphasis on immunohistochemistry and fluorescence analysis of tissue biomarkers. Digital pathology and image analysis have important roles across the drug/companion diagnostic development pipeline including biobanking, molecular pathology, tissue microarray analysis, molecular profiling of tissue and these important developments are reviewed. Underpinning all of these important developments is the need for high quality tissue samples and the impact of pre-analytical variables on tissue research is discussed. This requirement is combined with practical advice on setting up and running a digital pathology laboratory. Finally, we discuss the need to integrate digital image analysis data with epidemiological, clinical and genomic data in order to fully understand the relationship between genotype and phenotype and to drive discovery and the delivery of personalized medicine.

Consistency of arsenic speciation in global tobacco products with implications for health and regulation

Background: Tobacco smoke is a major risk to the health of its users and arsenic is among the components of smoke present at concentrations of toxicological concern. There are significant variations in human toxicity between inorganic and organic arsenic species and the aim of this study was to determine whether there are predictable relationships among major arsenic species in tobacco that could be useful for risk assessment.

Methods: 14 samples of tobacco were studied spanning a wide range of concentrations in samples from different geographical regions, including certified reference materials and cigarette products. Inorganic and major organic arsenic species were extracted from powdered tobacco samples by nitric acid using microwave digestion. Concentrations of arsenic species in these extracts were determined using HPLC-ICPMS.

Results: The concentrations of total inorganic arsenic species range from 144 to 3914 mu g kg(-1), while organic species dimethylarsinic acid (DMA) ranges from 21 to 176 mu g As kg(-1), and monomethylarsonic acid (MA) ranges from 30 to 116 mu g kg(-1). The percentage of species eluted compared to the total arsenic extracted ranges from 11.1 to 36.8% suggesting that some As species (possibly macro-molecules, strongly complexed or in organic forms) do not elute from the column. This low percentage of column-speciated arsenic is indicative that more complex forms of arsenic exist in the tobacco. All the analysed species correlate positively with total arsenic concentration over the whole compositional range and regression analysis indicates a consistent ratio of about 4:1 in favour of inorganic arsenic compared with MA + DMA.

Conclusions: The dominance of inorganic arsenic species among those components analysed is a marked feature of the diverse range of tobaccos selected for study. Such consistency is important in the context of a WHO expert panel recommendation to regulate tobacco crops and products using total arsenic concentration. If implemented more research would be required to develop models that accurately predict the smoker's exposure to reduced inorganic arsenic species on the basis of leaf or product concentration and product design features.

Re-Visiting Sylvia Townsend Warner

Sylvia Townsend Warner was born in 1893 in Harrow and died in Dorset in 1978. Her writing career was both productive and diverse, spanning poems, short stories, novels, music reviews, a biography, translations of Proust, and a guide to Somerset. But this list, impressive as it is, does not do justice to the idiosyncrasy and heterogeneity of her work. While she is well known mostly for the seven novels she published, those works are all radically different in style and content. Indeed, Townsend Warner's singularity has, it could be argued, made it difficult to place her in the various fields and sub-fields of 20th-century literary studies. She shares as many similarities as differences with the high modernists who dominated the literary landscape of the interwar period. Likewise she fits, yet also resists, the more recent formulations of intermodernist and middlebrow scholarship that have attempted to interrogate and expand the horizons of mid-20th century literature.