Pathotypic diversity of Hyaloperonospora brassicae collected from Brassica oleracea

Downy mildew caused by Hyaloperonospora brassicae is an economically destructive disease of brassica crops in many growing regions throughout the world. Specialised pathogenicity of downy mildews from different Brassica species and closely related ornamental or wild relatives has been described from host range studies. Pathotypic variation amongst Hyaloperonospora brassicae isolates from Brassica oleracea has also been described; however, a standard set of B. oleracea lines that could enable reproducible classification of H. brassicae pathotypes was poorly developed. For this purpose, we examined the use of eight genetically refined host lines derived from our previous collaborative work on downy mildew resistance as a differential set to characterise pathotypes in the European population of H. brassicae. Interaction phenotypes for each combination of isolate and host line were assessed following drop inoculation of cotyledons and a spectrum of seven phenotypes was observed based on the level of sporulation on cotyledons and visible host responses. Two host lines were resistant or moderately resistant to the entire collection of isolates, and another was universally susceptible. Five lines showed differential responses to the H. brassicae isolates. A minimum of six pathotypes and five major effect resistance genes are proposed to explain all of the observed interaction phenotypes. The B. oleracea lines from this study can be useful for monitoring pathotype frequencies in H. brassicae populations in the same or other vegetable growing regions, and to assess the potential durability of disease control from different combinations of the predicted downy mildew resistance genes

Spatial patterns and temporal variability of drought in Western Iran

An analysis of drought in western Iran from 1966 to 2000 is presented using monthly precipitation data observed at 140 gauges uniformly distributed over the area. Drought conditions have been assessed by means of the Standardized Precipitation Index (SPI). To study the long-term drought variability the principal component analysis was applied to the SPI field computed on 12-month time scale. The analysis shows that applying an orthogonal rotation to the first two principal component patterns, two distinct sub-regions having different climatic variability may be identified. Results have been compared to those obtained for the largescale using re-analysis data suggesting a satisfactory agreement. Furthermore, the extension of the large-scale analysis to a longer period (1948–2007) shows that the spatial patterns and the associated time variability of drought are subjected to noticeable changes. Finally, the relationship between hydrological droughts in the two sub-regions and El Niño Southern Oscillation events has been investigated finding that there is not clear evidence for a link between the two phenomen

FAN1 controls mismatch repair complex assembly via MLH1 retention to stabilize CAG repeat expansion in Huntington's disease

CAG repeat expansion in the HTT gene drives Huntington’s disease (HD) pathogenesis and is modulated by DNA damage repair pathways. In this context, the interaction between FAN1, a DNA-structure-specific nuclease, and MLH1, member of the DNA mismatch repair pathway (MMR), is not defined. Here, we identify a highly conserved SPYF motif at the N terminus of FAN1 that binds to MLH1. Our data support a model where FAN1 has two distinct functions to stabilize CAG repeats. On one hand, it binds MLH1 to restrict its recruitment by MSH3, thus inhibiting the assembly of a functional MMR complex that would otherwise promote CAG repeat expansion. On the other hand, it promotes accurate repair via its nuclease activity. These data highlight a potential avenue for HD therapeutics in attenuating somatic expansion

Emergent quantum confinement at topological insulator surfaces

Bismuth-chalchogenides are model examples of three-dimensional topological insulators. Their ideal bulk-truncated surface hosts a single spin-helical surface state, which is the simplest possible surface electronic structure allowed by their non-trivial $\mathbb{Z}_2$ topology. They are therefore widely regarded ideal templates to realize the predicted exotic phenomena and applications of this topological surface state. However, real surfaces of such compounds, even if kept in ultra-high vacuum, rapidly develop a much more complex electronic structure whose origin and properties have proved controversial. Here, we demonstrate that a conceptually simple model, implementing a semiconductor-like band bending in a parameter-free tight-binding supercell calculation, can quantitatively explain the entire measured hierarchy of electronic states. In combination with circular dichroism in angle-resolved photoemission (ARPES) experiments, we further uncover a rich three-dimensional spin texture of this surface electronic system, resulting from the non-trivial topology of the bulk band structure. Moreover, our study reveals how the full surface-bulk connectivity in topological insulators is modified by quantum confinement.Comment: 9 pages, including supplementary information, 4+4 figures. A high resolution version is available at http://www.st-andrews.ac.uk/~pdk6/pub_files/TI_quant_conf_high_res.pd

Integration of aqueous (micellar) two-phase systems on the proteins separation

A two-step approach combining an aqueous two-phase system (ATPS) and an aqueous micellar two-phase system (AMTPS), both based on the thermo-responsive copolymer Pluronic L-35, is here proposed for the purification of proteins and tested on the sequential separation of three model proteins, cytochrome c, ovalbumin and azocasein. Phase diagrams were established for the ATPS, as well as co-existence curves for the AMTPS. Then, by scanning and choosing the most promising systems, the separation of the three model proteins was performed. The aqueous systems based on Pluronic L-35 and potassium phosphate buffer (pH = 6.6) proved to be the most selective platform to separate the proteins (SAzo/Cyt = 1667; SOva/Cyt = 5.33 e SAzo/Ova = 1676). The consecutive fractionation of these proteins as well as their isolation from the aqueous phases was proposed, envisaging the industrial application of this downstream strategy. The environmental impact of this downstream process was studied, considering the carbon footprint as the final output. The main contribution to the total carbon footprint comes from the ultrafiltration (~ 49%) and the acid precipitation (~ 33%) due to the energy consumption in the centrifugation. The ATPS step contributes to ~ 17% while the AMTPS only accounts for 0.30% of the total carbon footprint.publishe

Phenotypic redshifts with self-organizing maps: A novel method to characterize redshift distributions of source galaxies for weak lensing

Wide-field imaging surveys such as the Dark Energy Survey (DES) rely on coarse measurements of spectral energy distributions in a few filters to estimate the redshift distribution of source galaxies. In this regime, sample variance, shot noise, and selection effects limit the attainable accuracy of redshift calibration and thus of cosmological constraints. We present a new method to combine wide-field, few-filter measurements with catalogs from deep fields with additional filters and sufficiently low photometric noise to break degeneracies in photometric redshifts. The multi-band deep field is used as an intermediary between wide-field observations and accurate redshifts, greatly reducing sample variance, shot noise, and selection effects. Our implementation of the method uses self-organizing maps to group galaxies into phenotypes based on their observed fluxes, and is tested using a mock DES catalog created from N-body simulations. It yields a typical uncertainty on the mean redshift in each of five tomographic bins for an idealized simulation of the DES Year 3 weak-lensing tomographic analysis of $\sigma_{\Delta z} = 0.007$, which is a 60% improvement compared to the Year 1 analysis. Although the implementation of the method is tailored to DES, its formalism can be applied to other large photometric surveys with a similar observing strategy.Comment: 24 pages, 11 figures; matches version accepted to MNRA

Optical types of inland and coastal waters

Inland and coastal waterbodies are critical components of the global biosphere. Timely monitoring is necessary to enhance our understanding of their functions, the drivers impacting on these functions and to deliver more effective management. The ability to observe waterbodies from space has led to Earth observation (EO) becoming established as an important source of information on water quality and ecosystem condition. However, progress toward a globally valid EO approach is still largely hampered by inconsistences over temporally and spatially variable in-water optical conditions. In this study, a comprehensive dataset from more than 250 aquatic systems, representing a wide range of conditions, was analyzed in order to develop a typology of optical water types (OWTs) for inland and coastal waters. We introduce a novel approach for clustering in situ hyperspectral water reflectance measurements (n = 4045) from multiple sources based on a functional data analysis. The resulting classification algorithm identified 13 spectrally distinct clusters of measurements in inland waters, and a further nine clusters from the marine environment. The distinction and characterization of OWTs was supported by the availability of a wide range of coincident data on biogeochemical and inherent optical properties from inland waters. Phylogenetic trees based on the shapes of cluster means were constructed to identify similarities among the derived clusters with respect to spectral diversity. This typification provides a valuable framework for a globally applicable EO scheme and the design of future EO missions

Development and validation of a population-based prediction scale for osteoporotic fracture in the region of Valencia, Spain: the ESOSVAL-R study

<p>Abstract</p> <p>Background</p> <p>Today, while there are effective drugs that reduce the risk of osteoporotic fracture, yet there are no broadly accepted criteria that can be used to estimate risks and decide who should receive treatment. One of the actual priorities of clinical research is to develop a set of simple and readily-available clinical data that can be used in routine clinical practice to identify patients at high risk of bone fracture, and to establish thresholds for therapeutic interventions. Such a tool would have high impact on healthcare policies. The main objective of the ESOSVAL-R is to develop a risk prediction scale of osteoporotic fracture in adult population using data from the Region of Valencia, Spain.</p> <p>Methods/Design</p> <p><it>Study design</it>: An observational, longitudinal, prospective cohort study, undertaken in the Region of Valencia, with an initial follow-up period of five years; <it>Subjects</it>: 14,500 men and women over the age of 50, residing in the Region and receiving healthcare from centers where the ABUCASIS electronic clinical records system is implanted; <it>Sources of data</it>: The ABUCASIS electronic clinical record system, complemented with hospital morbidity registers, hospital Accidents & Emergency records and the Regional Ministry of Health's mortality register; <it>Measurement of results</it>: Incident osteoporotic fracture (in the hip and/or major osteoporotic fracture) during the study's follow-up period. Independent variables include clinical data and complementary examinations; <it>Analysis</it>: 1) Descriptive analysis of the cohorts' baseline data; 2) Upon completion of the follow-up period, analysis of the strength of association between the risk factors and the incidence of osteoporotic fracture using Cox's proportional hazards model; 3) Development and validation of a model to predict risk of osteoporotic fracture; the validated model will serve to develop a simplified scale that can be used during routine clinical visits.</p> <p>Discussion</p> <p>The ESOSVAL-R study will establish a prediction scale for osteoporotic fracture in Spanish adult population. This scale not only will constitute a useful prognostic tool, but also it will allow identifying intervention thresholds to support treatment decision-making in the Valencia setting, based mainly on the information registered in the electronic clinical records.</p

Mechanisms and age estimates of continental-scale endorheic to exorheic drainage transition: Douro River, Western Iberia

In western Iberia, mechanisms that can explain the transition from endorheic to exorheic continental-scale drainage reorganization are foreland basin overspill, headwards erosion and capture by an Atlantic river, or a combination of both. To explore these, we have investigated the Portuguese sector of the Douro River, the locus of drainage reorganization. The Douro River is routed downstream through the weak sedimentary infill of the Douro Cenozoic Basin, after which the river cuts down through harder granitic and metamorphic rocks crossed by active fault zones, before reaching the Atlantic coast. We investigated the drainage reorganization using an integrated approach that combined remote sensing, field survey and geochronology, applied to Pliocene–Quaternary fluvial sediments and landforms. The older drainage record is documented by a series of high and intermediate landform levels comprising: (1) a high level (1000–500 m a.s.l.) faulted regional fluvial erosion surface, the North Iberian Meseta planation surface and the Mountains and Plateaus of Northern Portugal, recording the endorheic drainage of the Douro Cenozoic Basin; (2) a first inset level at 650–600 m a.s.l., comprising a broad fluvial surface developed onto a large ENE–WSW depression, interpreted as recording the initiation of the continental scale reorganization; and (3) an inset fluvial surface at 550–400 m a.s.l., corresponding to the establishment of the exorheic ancestral Douro valley. The younger drainage record comprises an entrenched fluvial strath terrace sequence of up to 9 levels (T9 = oldest), positioned at 246–242 m above the modern river base; T1 = youngest, positioned at +17–13 m. Levels T1 and T3 display localized fault offsets. The three lowest terrace levels (T3–T1) were dated using optically stimulated luminescence techniques with results ranging from >230–360 ka (T3), through 57 ka (T2) to 39–12 ka (T1). Fluvial incision rates of the younger terraces were quantified and temporally extrapolated to model the ages of the intermediate to high elevation levels of the early drainage record. Integration of incision data informs on the probable timing of the drainage reorganization and the initial adjustment, ~3.7–1.8 Ma. This was followed by acceleration of incision, producing the entrenched river terrace sequence developed via spatial and temporal variations in rock strength, uplift and cyclic cool-climate variability as the river adjusted to the Atlantic base level