Isothermal Recombinase Polymerase amplification (RPA) of Schistosoma haematobium DNA and oligochromatographic lateral flow detection

© 2015 Rosser et al. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. The attached file is the published version of the article

Lanthanides in granulometric fractions of Mediterranean soils. Can they be used as fingerprints of provenance?

Highlights Are lanthanides from fine sand and clay genetically related to the geological materials? Lanthanide concentrations of fine sand and clay fit chronofunctions Pearson's r of lanthanide couples decreases when separation increases in the periodic table Free forms of clay are scavengers of lanthanides and concentrate HREE and ceriumSample preparation and chemical analysis were conducted by Emma Humphreys-Williams and Stanislav Strekopytov (Imaging and Analysis Centre, Natural History Museum, London, UK). This work was supported by a grant from Ministerio de Economía, Industria y Competitividad de España (‘Tipologías de Suelos Mediterráneos versus Cuarzo. En la frontera del conocimiento edafogenético’; Ref. CGL2016-80308-P). The authors thank Professor Margaret A. Oliver, an anonymous editor and two anonymous reviewers for helpful comments and suggestions that improved the final manuscript. We also thank Robert Abrahams (Bsc) for revising the English language.There is geochemical interest in the lanthanides because they behave like a group that is closely related to the parent materials during surface processes, although they also undergo fractionation as a result of supergene dynamics. We analysed lanthanide concentrations (ICPms) in the granulometric fractions fine sand, clay and free forms of clay (FFclay‐CDB and FFclay‐Ox: extracted with citrate‐dithionite‐sodium bicarbonate and with ammonium oxalate, respectively) from a soil chronosequence of Mediterranean soils. There was a relative enrichment of heavy rare earth elements (HREE) in the clay fraction and its free forms with respect to fine sand. The clay free forms behaved as scavengers of lanthanides, and oxidative scavenging of cerium (Ce) in FFclay‐CDB was also detected. Lanthanide concentrations (lanthanum to gadolinium in fine sand; terbium to lutetium in clay) varied with soil age, and chronofunctions were established. There was a strong positive collinearity between most of the lanthanide concentrations. Furthermore, the value of the correlation index (Pearson's r ) of the concentrations between couples of lanthanides (r CLC) decreased significantly with increasing separation between the elements in the periodic table; this has never been described in soils. Several geochemical properties and indices in the fine sand and clay soil fractions and in the geological materials of the Guadalquivir catchment showed, on the one hand, a genetic relation between them all, enabling the lanthanides to be used as fingerprints of provenance; on the other hand, fractionation between fine sand and clay showed these are actively involved in soil lanthanide dynamics.Secretaría de Estado de Investigación, Desarrollo e Innovación. Grant Number: CGL2016‐80308‐

Development of novel multiplex microsatellite polymerase chain reactions to enable high-throughput population genetic studies of Schistosoma haematobium

© 2015 Webster et al. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. The attached file is the published version of the article

How Do Climate Change Experiments Alter Plot-Scale Climate?

To understand and forecast biological responses to climate change, scientists frequently use field experiments that alter temperature and precipitation. Climate manipulations can manifest in complex ways, however, challenging interpretations of biological responses. We reviewed publications to compile a database of daily plot-scale climate data from 15 active-warming experiments. We find that the common practices of analysing treatments as mean or categorical changes (e.g. warmed vs.unwarmed) masks important variation in treatment effects over space and time. Our synthesis showed that measured mean warming, in plots with the same target warming within a study, differed by up to 1.6 Celsius degrees (63% of target), on average, across six studies with blocked designs. Variation was high across sites and designs: for example, plots differed by 1.1Celsius degrees (47% of target) on average, for infrared studies with feedback control (n = 3) vs. by 2.2 Celsius degrees (80% of target) on average for infrared with constant wattage designs (n = 2). Warming treatments produce non-temperature effects as well, such as soil drying. The combination of these direct and indirect effects is complex and can have important biological consequences. With a case study of plant phenology across five experiments in our database, we show how accounting for drier soils with warming tripled the estimated sensitivity of budburst to temperature. We provide recommendations for future analyses, experimental design,and data sharing to improve our mechanistic understanding from climate change experiments, and thus their utility to accurately forecast species' responses

Variation at GRN 3′-UTR rs5848 Is Not Associated with a Risk of Frontotemporal Lobar Degeneration in Dutch Population

Background: A single nucleotide polymorphism (rs5848) located in the 3′- untranslated region of GRN has recently been associated with a risk of frontotemporal lobar degeneration (FTLD) in North American population particularly in pathologically confirmed cases with neural inclusions immunoreactive for ubiquitin and TAR DNA-binding protein 43 (TDP-43), but negative for tau and alpha-synuclein (FTLD-TDP). Methodology/Principal Findings: In an effort to replicate these results in a different population, rs5848 was genotyped in 256 FTLD cases and 1695 controls from the Netherlands. Single SNP gender-adjusted logistic regression analysis revealed no significant association between variation at rs5848 and FTLD. Fisher's exact test, failed to find any significant association between rs5848 and a subset of 23 pathology confirmed FTLD-TDP cases. Conclusions/Significance: The evidence presented here suggests that variation at rs5848 does not contribute to the etiology of FTLD in the Dutch population

Organisational culture of further education colleges delivering higher education business programmes: developing a culture of ‘HEness’ – what next?

This paper draws on the views of lecturers working in and delivering college-based higher education (CBHE) in the UK. There have been numerous works on the culture of higher education in further education (HE in FE). However, as noted by some literati, the culture of further education (FE) is not easy to define, and does not readily lend itself to the incorporation of a higher education (HE) culture. This could be due to the large number of changes FE has had to adopt owing to various government policies. The study comprises 26 in-depth individual interviews conducted at various further education colleges throughout the Yorkshire and Humber region of the UK. Via the use of an interpretivist approach, common themes and word use were extracted from the narratives for analysis. The organisational culture of these further education colleges was relatively easy to define, the word ‘blame’ being one of the common themes. However, when identifying if the individual colleges had a HE culture; this proved more difficult

Potential drivers for schistosomiasis persistence: population genetic analyses from a cluster-randomized urogenital schistosomiasis elimination trial across the Zanzibar islands

The World Health Organization's revised NTD Roadmap and the newly launched Guidelines target elimination of schistosomiasis as a public health problem in all endemic areas by 2030. Key to meeting this goal is elucidating how selective pressures imposed by interventions shape parasite populations. Our aim was to identify any differential impact of a unique cluster-randomized tri-armed elimination intervention (biannual mass drug administration (MDA) applied alone or in association with either mollusciciding (snail control) or behavioural change interventions) across two Zanzibarian islands (Pemba and Unguja) on the population genetic composition of Schistosoma haematobium over space and time. Fifteen microsatellite loci were used to analyse individual miracidia collected from infected individuals across islands and intervention arms at the start (2012 baseline: 1,522 miracidia from 176 children; 303 from 43 adults; age-range 6-75, mean 12.7 years) and at year 5 (2016: 1,486 miracidia from 146 children; 214 from 25 adults; age-range 9-46, mean 12.4 years). Measures of genetic diversity included allelic richness (Ar), Expected (He) and Observed heterozygosity (Ho), inbreeding coefficient (FST), parentage analysis, estimated worm burden, worm fecundity, and genetic sub-structuring. There was little evidence of differential selective pressures on population genetic diversity, inbreeding or estimated worm burdens by treatment arm, with only the MDA+snail control arm within Unguja showing trends towards reduced diversity and altered inbreeding over time. The greatest differences overall, both in terms of parasite fecundity and genetic sub-structuring, were observed between the islands, consistent with Pemba's persistently higher mean infection intensities compared to neighbouring Unguja, and within islands in terms of infection hotspots (across three definitions). These findings highlight the important contribution of population genetic analyses to elucidate extensive genetic diversity and biological drivers, including potential gene-environmental factors, that may override short term selective pressures imposed by differential disease control strategies. Trial Registration: ClinicalTrials.gov ISRCTN48837681

Ancient hybridization and adaptive introgression of an invadolysin gene in schistosome parasites

Introgression among parasite species has the potential to transfer traits of biomedical importance across species boundaries. The parasitic blood fluke Schistosoma haematobium causes urogenital schistosomiasis in humans across sub-Saharan Africa. Hybridization with other schistosome species is assumed to occur commonly, because genetic crosses between S. haematobium and livestock schistosomes, including S. bovis, can be staged in the laboratory, and sequencing of mtDNA and rDNA amplified from microscopic miracidia larvae frequently reveals markers from different species. However the frequency, direction, age and genomic consequences of hybridization are unknown. We hatched miracidia from eggs, and sequenced the exomes from 96 individual S. haematobium miracidia from infected patients from Niger and the Zanzibar archipelago. These data revealed no evidence for contemporary hybridization between S. bovis and S. haematobium in our samples. However, all Nigerien S. haematobium genomes sampled show hybrid ancestry, with 3.3-8.2% of their nuclear genomes derived from S. bovis, providing evidence of an ancient, introgression event that occurred at least 108-613 generations ago. Some S. bovis derived alleles have spread to high frequency or reached fixation and show strong signatures of directional selection; the strongest signal spans a single gene in the invadolysin gene family (Chr. 4). Our results suggest that S. bovis/S. haematobium hybridization occurs rarely, but demonstrate profound consequences of ancient introgression from a livestock parasite into the genome of S. haematobium, the most prevalent schistosome species infecting humans

Seasonality of nitrogen sources, cycling, and loading in a New England river discerned from nitrate isotope ratios

Coastal waters globally are increasingly impacted due to the anthropogenic loading of nitrogen (N) from the watershed. To assess dominant sources contributing to the eutrophication of the Little Narragansett Bay estuary in New England, we carried out an annual study of N loading from the Pawcatuck River. We conducted weekly monitoring of nutrients and nitrate (NO3-) isotope ratios (15N / 14N, 18O / 16O, and 17O / 16O) at the mouth of the river and from the larger of two wastewater treatment facilities (WWTFs) along the estuary, as well as seasonal along-river surveys. Our observations reveal a direct relationship between N loading and the magnitude of river discharge and a consequent seasonality to N loading into the estuary – rendering loading from the WWTFs and from an industrial site more important at lower river flows during warmer months, comprising ∼ 23 % and ∼ 18 % of N loading, respectively. Riverine nutrients derived predominantly from deeper groundwater and the industrial point source upriver in summer and from shallower groundwater and surface flow during colder months – wherein NO3- associated with deeper groundwater had higher 15N / 14N ratios than shallower groundwater. Corresponding NO3- 18O / 16O ratios were lower during the warm season, due to increased biological cycling in-river. Uncycled atmospheric NO3-, detected from its unique mass-independent NO3- 17O / 16O vs. 18O / 16O fractionation, accounted for &lt; 3 % of riverine NO3-, even at elevated discharge. Along-river, NO3- 15N / 14N ratios showed a correspondence to regional land use, increasing from agricultural and forested catchments to the more urbanized watershed downriver. The evolution of 18O / 16O isotope ratios along-river conformed to the notion of nutrient spiraling, reflecting the input of NO3- from the catchment and from in-river nitrification and its coincident removal by biological consumption. These findings stress the importance of considering seasonality of riverine N sources and loading to mitigate eutrophication in receiving estuaries. Our study further advances a conceptual framework that reconciles with the current theory of riverine nutrient cycling, from which to robustly interpret NO3- isotope ratios to constrain cycling and source partitioning in river systems.</p