High-resolution genome-wide cytosine methylation profiling with simultaneous copy number analysis and optimization for limited cell numbers

Many genome-wide assays involve the generation of a subset (or representation) of the genome following restriction enzyme digestion. The use of enzymes sensitive to cytosine methylation allows high-throughput analysis of this epigenetic regulatory process. We show that the use of a dual-adapter approach allows us to generate genomic representations that includes fragments of <200bp in size, previously not possible when using the standard approach of using a single adapter. By expanding the representation to smaller fragments using HpaII or MspI, we increase the representation by these isoschizomers to more than 1.32 million loci in the human genome, representing 98.5% of CpG islands and 91.1% of refSeq promoters. This advance allows the development of a new, high-resolution version of our HpaII-tiny fragment Enrichment by Ligation-mediated PCR (HELP) assay to study cytosine methylation. We also show that the MspI representation generates information about copy-number variation, that the assay can be used on as little as 10ng of DNA and that massively parallel sequencing can be used as an alternative to microarrays to read the output of the assay, making this a powerful discovery platform for studies of genomic and epigenomic abnormalities.     

Variation in Glucose-6-Phosphate Dehydrogenase activity following acute malaria

Primaquine and tafenoquine are the only licensed drugs with activity against Plasmodium vivax hypnozoites but cause haemolysis in patients with glucose–6–phosphate dehydrogenase (G6PD) deficiency. Malaria also causes haemolysis, leading to the replacement of older erythrocytes with low G6PD activity by reticulocytes and young erythrocytes with higher activity. Aim of this study was to assess the impact of acute malaria on G6PD activity. Selected patients with uncomplicated malaria were recruited in Bangladesh (n = 87), Indonesia (n = 75), and Ethiopia (n = 173); G6PD activity was measured at the initial presentation with malaria and a median of 176 days later (range 140 to 998) in the absence of malaria. Among selected participants (deficient participants preferentially enrolled in Bangladesh but not at other sites) G6PD activity fell between malaria and follow up by 79.1% (95%CI: 40.4 to 117.8) in 6 participants classified as deficient (<30% activity), 43.7% (95%CI: 34.2 to 53.1) in 39 individuals with intermediate activity (30% to <70%), and by 4.5% (95%CI: 1.4 to 7.6) in 290 G6PD normal (≥70%) participants. In Bangladesh and Indonesia G6PD activity was significantly higher during acute malaria than when the same individuals were retested during follow up (40.9% (95%CI: 33.4–48.1) and 7.4% (95%CI: 0.2 to 14.6) respectively), whereas in Ethiopia G6PD activity was 3.6% (95%CI: -1.0 to -6.1) lower during acute malaria. The change in G6PD activity was apparent in patients presenting with either P. vivax or P. falciparum infection. Overall, 66.7% (4/6) severely deficient participants and 87.2% (34/39) with intermediate deficiency had normal activities when presenting with malaria.These findings suggest that G6PD activity rises significantly and at clinically relevant levels during acute malaria. Prospective case-control studies are warranted to confirm the degree to which the predicted population attributable risks of drug induced haemolysis is lower than would be predicted from cross sectional surveys.     

Modeling the role of the close‐range effect and environmental variables in the occurrence and spread of Phragmites australis in four sites on the Finnish coast of the Gulf of Finland and the Archipelago Sea

Phragmites australis, a native helophyte in coastal areas of the Baltic Sea, has significantly spread on the Finnish coast in the last decades raising ecological questions and social interest and concern due to the important role it plays in the ecosystem dynamics of shallow coastal areas. Despite its important implications on the planning and management of the area, predictive modeling of Phragmites distribution is not well studied. We examined the prevalence and progression of Phragmites in four sites along the Southern Finnish coast in multiple time frames in relation to a number of predictors. We also analyzed patterns of neighborhood effect on the expansion and disappearance of Phragmites in a cellular data model. We developed boosted regression trees models to predict Phragmites occurrences and produce maps of habitat suitability. Various Phragmites spread figures were observed in different areas and time periods, with a minimum annual expansion rate of 1% and a maximum of 8%. The water depth, shore openness, and proximity to river mouths were found influential in Phragmites distribution. The neighborhood configuration partially explained the dynamics of Phragmites colonies. The boosted regression trees method was successfully used to interpolate and extrapolate Phragmites distributions in the study sites highlighting its potential for assessing habitat suitability for Phragmites along the Finnish coast. Our findings are useful for a number of applications. With variables easily available, delineation of areas susceptible for Phragmites colonization allows early management plans to be made. Given the influence of reed beds on the littoral species and ecosystem, these results can be useful for the ecological studies of coastal areas. We provide estimates of habitat suitability and quantification of Phragmites expansion in a form suitable for dynamic modeling, which would be useful for predicting future Phragmites distribution under different scenarios of land cover change and Phragmites spatial configuration.     

The effects of prey demography on humpback whale (Megaptera novaeangliae) abundance around Anvers Island, Antarctica

Baleen whales and Adelie penguins in the near-shore waters around the Antarctic Peninsula forage principally on Antarctic krill. Given the spatial overlap in the distribution of these krill predators (particularly humpback whales) and their dependence on krill, the goals of this paper are to determine if the inter-annual community structure and relative abundance of baleen whales around Anvers Island is related to krill demography and abundance, and if the potential exists for inter-specific interactions between Adelie penguins and baleen. We use whale sightings and prey data from both net tows and Adelie penguin stomach samples to correlate the abundance of humpback whales with krill demography and abundance from 1993 to 2001. We find significant relationships between whale abundance and the size–frequency distribution of krill targeted by Adelie penguins, as well as the foraging success of Adelie penguins. These findings suggest both krill predators share common prey preferences in the upper portions of the water column around Anvers Island. These findings highlight the need for better knowledge of baleen whale foraging ecology and inter-specific interactions with penguins, as sea ice and krill populations around the Antarctic Peninsula are affected by rapid changes in climate.     

Estimating dengue transmission intensity from serological data: A comparative analysis using mixture and catalytic models

BackgroundDengue virus (DENV) infection is a global health concern of increasing magnitude. To target intervention strategies, accurate estimates of the force of infection (FOI) are necessary. Catalytic models have been widely used to estimate DENV FOI and rely on a binary classification of serostatus as seropositive or seronegative, according to pre-defined antibody thresholds. Previous work has demonstrated the use of thresholds can cause serostatus misclassification and biased estimates. In contrast, mixture models do not rely on thresholds and use the full distribution of antibody titres. To date, there has been limited application of mixture models to estimate DENV FOI.MethodsWe compare the application of mixture models and time-constant and time-varying catalytic models to simulated data and to serological data collected in Vietnam from 2004 to 2009 (N ≥ 2178) and Indonesia in 2014 (N = 3194).ResultsThe simulation study showed larger mean FOI estimate bias from the time-constant and time-varying catalytic models (-0.007 (95% Confidence Interval (CI): -0.069, 0.029) and -0.006 (95% CI -0.095, 0.043)) than from the mixture model (0.001 (95% CI -0.036, 0.065)). Coverage of the true FOI was > 95% for estimates from both the time-varying catalytic and mixture model, however the latter had reduced uncertainty. When applied to real data from Vietnam, the mixture model frequently produced higher FOI and seroprevalence estimates than the catalytic models.ConclusionsOur results suggest mixture models represent valid, potentially less biased, alternatives to catalytic models, which could be particularly useful when estimating FOI from data with largely overlapping antibody titre distributions.     

Phosphorylation and inactivation of rat hepatocyte glycogen synthase by phorbol esters and mezerein

Incubation of rat hepatocytes with active phorbol esters and mezerein provoked a decrease in glycogen synthase activity. After the incubation of [3 2 P] phosphate-labeled cells with these tumor promoters, an increase in the amount of 3 2 P bound to the immunoprecipitated enzyme was observed. The decrease in activity highly correlated with the phosphorylation in the smaller CNBr fragment (CB-1) and only at high concentration of the phorbol ester the increase in the phosphorylation of the larger CNBr fragment (CB-2) became significative. Tryptic degradation of CB-1 showed two phosphopeptides after isoelectro focusing analysis (pI 3.9 and pI 3.4) and only one of them (pI 3.9) increased its phosphorylation state after treatment of the cells. These results indicate that the decrease in activity of glycogen synthase by phorbol esters and mezerein is a result of the phosphorylation of the enzyme and that a single site located in CB-1 is preferentially phosphorylated by these agents.     

Antibodies to listeriolysin O reflect the acquired resistance to Listeria monocytogenes in experimentally infected goats

We induced experimental listeriosis in goats by two sequential oral inoculations of Listeria monocytogenes serovar 1/2a at 8 months' interval. Immunoblot analysis with the goat sera demonstrated listeriolysin O (LLO) as the principal protein antigen of L. monocytogenes. Pre-existing antibodies to LLO were, depending on their initial level, associated with either mild clinical symptoms of short duration or the total absence of clinical symptoms. Similarly, the presence and development of such antibodies corresponded with the disappearance pattern of L. monocytogenes from the gastrointestinal tract. These findings suggest that an association exists between antibodies to LLO and acquired resistance to Listeria infections.