Refinement of the critical region for MCKD1 by detection of transcontinental haplotype sharing

Refinement of the critical region for MCKD1 by detection of transcontinental haplotype sharing.BackgroundAutosomal-dominant medullary cystic kidney disease type 1 (MCKD1) [OMIM 174000] is a hereditary nephropathy that leads to renal salt wasting and end-stage renal failure at a median age of 62 years. In a Welsh MCKD1 kindred we have recently demonstrated linkage to the MCKD1 locus on chromosome 1q23.1 and refined the critical MCKD1 region to <3.3Mb.MethodsIn order to refine the candidate gene region for MCKD1, high-resolution haplotype analysis in three large kindreds with MCKD1 was performed.ResultsWe report here on high-resolution haplotype analysis in this Welsh kindred, as well as in the Arizona kindred, which was used for the first definition of MCKD as a disease entity, and in a kindred from the Dutch/German border. We detected extensive haplotype sharing among all affected individuals of all three kindreds. Scrutinization of the genealogy of the Arizona kindred revealed an origin from Germany in the 17th century, thereby providing historical data for haplotype sharing by descent at the MCKD1 locus.ConclusionUnder the hypothesis of haplotype sharing by descent, we refined the critical genetic interval to <650kb, thus enabling candidate gene analysis

Characterization of human cytomegalovirus genome diversity in immunocompromised hosts by whole genomic sequencing directly from clinical specimens

Background: Advances in next-generation sequencing (NGS) technologies allow comprehensive studies of genetic diversity over the entire genome of human cytomegalovirus (HCMV), a significant pathogen for immunocompromised individuals. Methods: NGS was performed on target-enriched sequence libraries prepared directly from a variety of clinical specimens (blood, urine, breast-milk, respiratory samples, biopsies and vitreous humor) obtained longitudinally or from different anatomical compartments from 20 HCMV-infected patients (renal transplant recipients, stem cell transplant recipients and congenitally infected children). Results: De novo assembled HCMV genome sequences were obtained for 57/68 sequenced samples. Analysis of longitudinal or compartmental HCMV diversity revealed various patterns: no major differences were detected among longitudinal, intra-individual blood samples from 9/15 patients and in most of the patients with compartmental samples, whereas a switch of the major HCMV population was observed in six individuals with sequential blood samples and upon compartmental analysis of one patient with HCMV retinitis. Variant analysis revealed additional aspects of minor virus population dynamics and antiviral resistance mutations. Conclusions: In immunosuppressed patients, HCMV can remain relatively stable or undergo drastic genomic changes that are suggestive of the emergence of minor resident strains or de novo infection

The influence of C3 and C4 vegetation on soil organic matter dynamics in contrasting semi-natural tropical ecosystems

This is a freely-available open access publication. Please cite the published version which is available via the DOI link in this record.Variations in the carbon isotopic composition of soil organic matter (SOM) in bulk and fractionated samples were used to assess the influence of C3 and C4 vegetation on SOM dynamics in semi-natural tropical ecosystems sampled along a precipitation gradient in West Africa. Differential patterns in SOM dynamics in C3/C4 mixed ecosystems occurred at various spatial scales. Relative changes in C/ N ratios between two contrasting SOM fractions were used to evaluate potential site-scale differences in SOM dynamics between C3- and C4-dominated locations. These differences were strongly controlled by soil texture across the precipitation gradient, with a function driven by bulk δ 13C and sand content explaining 0.63 of the observed variability. The variation of δ 13C with soil depth indicated a greater accumulation of C3-derived carbon with increasing precipitation, with this trend also being strongly dependant on soil characteristics. The influence of vegetation thickening on SOM dynamics was also assessed in two adjacent, but structurally contrasting, transitional ecosystems occurring on comparable soils to minimise the confounding effects posed by climatic and edaphic factors. Radiocarbon analyses of sand-size aggregates yielded relatively short mean residence times (τ ) even in deep soil layers, while the most stable SOM fraction associated with silt and clay exhibited shorter τ in the savanna woodland than in the neighbouring forest stand. These results, together with the vertical variation observed in δ 13C values, strongly suggest that both ecosystems are undergoing a rapid transition towards denser closed canopy formations. However, vegetation thickening varied in intensity at each site and exerted contrasting effects on SOM dynamics. This study shows that the interdependence between biotic and abiotic factors ultimately determine whether SOM dynamics of Published by Copernicus Publications on behalf of the European Geosciences Union. 5042 G. Saiz et al.: Influence of C3/C4 on SOM in tropical biomes C3- and C4-derived vegetation are at variance in ecosystems where both vegetation types coexist. The results highlight the far-reaching implications that vegetation thickening may have for the stability of deep SOM.UK National Environment Research CouncilAustralian Institute of Nuclear Science and Engineering (AINSE Ltd

High Temperature Electron Localization in dense He Gas

We report new accurate mesasurements of the mobility of excess electrons in high density Helium gas in extended ranges of temperature $[(26\leq T\leq 77) K ]$ and density $[ (0.05\leq N\leq 12.0) {atoms} \cdot {nm}^{-3}]$ to ascertain the effect of temperature on the formation and dynamics of localized electron states. The main result of the experiment is that the formation of localized states essentially depends on the relative balance of fluid dilation energy, repulsive electron-atom interaction energy, and thermal energy. As a consequence, the onset of localization depends on the medium disorder through gas temperature and density. It appears that the transition from delocalized to localized states shifts to larger densities as the temperature is increased. This behavior can be understood in terms of a simple model of electron self-trapping in a spherically symmetric square well.Comment: 23 pages, 13 figure

Foliar trait contrasts between African forest and savanna trees: Genetic versus environmental effects

Journal ArticleVariations in leaf mass per unit area (Ma) and foliar concentrations of N, P, C, K, Mg and Ca were determined for 365 trees growing in 23 plots along a West African precipitation gradient ranging from 0.29 to 1.62m a-1. Contrary to previous studies, no marked increase in Ma with declining precipitation was observed, but savanna tree foliar [N] tended to be higher at the drier sites (mass basis). Generally, Ma was slightly higher and [N] slightly lower for forest vs savanna trees with most of this difference attributable to differences in soil chemistry. No systematic variations in [P], [Mg] and [Ca] with precipitation or between trees of forest vs savanna stands were observed. We did, however, find a marked increase in foliar [K] of savanna trees as precipitation declined, with savanna trees also having a significantly lower [K] than those of nearby forest. These differences were not related to differences in soil nutrient status and were accompanied by systematic changes in [C] of opposite sign. We suggest an important but as yet unidentified role for K in the adaption of savanna species to periods of limited water availability; with foliar [K] being also an important factor differentiating tree species adapted to forest vs savanna soils within the 'zone of transition' of Western Africa.Natural Environment Research Council TROBIT Consortium projectRoyal Society - University Research Fellowshi

Edaphic, structural and physiological contrasts across Amazon Basin forest-savanna ecotones suggest a role for potassium as a key modulator of tropical woody vegetation structure and function

Sampling along a precipitation gradient in tropical South America extending from ca. 0.8 to 2.0 m ag-1, savanna soils had consistently lower exchangeable cation concentrations and higher C/N ratios than nearby forest plots. These soil differences were also reflected in canopy averaged leaf traits with savanna trees typically having higher leaf mass per unit area but lower mass-based nitrogen (Nm) and potassium (Km). Both Nm and Km also increased with declining mean annual precipitation (PA), but most area-based leaf traits such as leaf photosynthetic capacity showed no systematic variation with PA or vegetation type. Despite this invariance, when taken in conjunction with other measures such as mean canopy height, area-based soil exchangeable potassium content, [K]sa , proved to be an excellent predictor of several photosynthetic properties (including 13C isotope discrimination). Moreover, when considered in a multivariate context with PA and soil plant available water storage capacity (θP) as covariates, [K]sa also proved to be an excellent predictor of stand-level canopy area, providing drastically improved fits as compared to models considering just PA and/or θP. Neither calcium, nor magnesium, nor soil pH could substitute for potassium when tested as alternative model predictors (ΔAIC > 10). Nor for any model could simple soil texture metrics such as sand or clay content substitute for either [K]sa or θP. Taken in conjunction with recent work in Africa and the forests of the Amazon Basin, this suggests-in combination with some newly conceptualised interacting effects of PA and θP also presented here-a critical role for potassium as a modulator of tropical vegetation structure and function.Natural Environment Research Council (NERC) TROBIT Consortium projectCNPqRoyal Society of London - Wolfson Research Merit Awar

Instrumentation and Measurement Strategy for the NOAA SENEX Aircraft Campaign as Part of the Southeast Atmosphere Study 2013

Natural emissions of ozone-and-aerosol-precursor gases such as isoprene and monoterpenes are high in the southeast of the US. In addition, anthropogenic emissions are significant in the Southeast US and summertime photochemistry is rapid. The NOAA-led SENEX (Southeast Nexus) aircraft campaign was one of the major components of the Southeast Atmosphere Study (SAS) and was focused on studying the interactions between biogenic and anthropogenic emissions to form secondary pollutants. During SENEX, the NOAA WP-3D aircraft conducted 20 research flights between 27 May and 10 July 2013 based out of Smyrna, TN. Here we describe the experimental approach, the science goals and early results of the NOAA SENEX campaign. The aircraft, its capabilities and standard measurements are described. The instrument payload is summarized including detection limits, accuracy, precision and time resolutions for all gas-and-aerosol phase instruments. The inter-comparisons of compounds measured with multiple instruments on the NOAA WP-3D are presented and were all within the stated uncertainties, except two of the three NO2 measurements. The SENEX flights included day- and nighttime flights in the Southeast as well as flights over areas with intense shale gas extraction (Marcellus, Fayetteville and Haynesville shale). We present one example flight on 16 June 2013, which was a daytime flight over the Atlanta region, where several crosswind transects of plumes from the city and nearby point sources, such as power plants, paper mills and landfills, were flown. The area around Atlanta has large biogenic isoprene emissions, which provided an excellent case for studying the interactions between biogenic and anthropogenic emissions. In this example flight, chemistry in and outside the Atlanta plumes was observed for several hours after emission. The analysis of this flight showcases the strategies implemented to answer some of the main SENEX science questions

Cherenkov radiation emitted by ultrafast laser pulses and the generation of coherent polaritons

We report on the generation of coherent phonon polaritons in ZnTe, GaP and LiTaO$_{3}$ using ultrafast optical pulses. These polaritons are coupled modes consisting of mostly far-infrared radiation and a small phonon component, which are excited through nonlinear optical processes involving the Raman and the second-order susceptibilities (difference frequency generation). We probe their associated hybrid vibrational-electric field, in the THz range, by electro-optic sampling methods. The measured field patterns agree very well with calculations for the field due to a distribution of dipoles that follows the shape and moves with the group velocity of the optical pulses. For a tightly focused pulse, the pattern is identical to that of classical Cherenkov radiation by a moving dipole. Results for other shapes and, in particular, for the planar and transient-grating geometries, are accounted for by a convolution of the Cherenkov field due to a point dipole with the function describing the slowly-varying intensity of the pulse. Hence, polariton fields resulting from pulses of arbitrary shape can be described quantitatively in terms of expressions for the Cherenkov radiation emitted by an extended source. Using the Cherenkov approach, we recover the phase-matching conditions that lead to the selection of specific polariton wavevectors in the planar and transient grating geometry as well as the Cherenkov angle itself. The formalism can be easily extended to media exhibiting dispersion in the THz range. Calculations and experimental data for point-like and planar sources reveal significant differences between the so-called superluminal and subluminal cases where the group velocity of the optical pulses is, respectively, above and below the highest phase velocity in the infrared.Comment: 13 pages, 11 figure