Using false discovery rates to benchmark SNP-callers in next-generation sequencing projects

Funding: R.A.F. was funded by the Natural Environment Research Council (NERC). D.A.H. and M.C.F. were supported by the Wellcome Trust. No additional external funding received for this study.Peer reviewedPublisher PD

Density of states within the bandgap of perovskite thin films studied using the moving grating technique

In this work, we further study the moving grating technique applied to halide perovskite thin-film materials. First, we show some problems that emerge when analyzing the experimental data with the classical formulation, which does not distinguish between free and trapped carriers and hence only gives average quantities for the transport parameters. We show that using a more general framework, taking into account the multiple trapping of carriers within a density of localized states, allows for an accurate description. Since it includes the density of states (DOS) of the material, it enables the possibility to test different DOS models proposed in the past for halide perovskite thin films. We check whether these models give rise to the type of curves we have measured under different experimental conditions. Finally, we propose a new model for the DOS in the forbidden gap, which results in the best fit found for the measurements performed. This allows us to give ranges of values for the parameters that define the DOS, which, as far as we know, are given for the first time

Chromosomal copy number variation, selection and uneven rates of recombination reveal cryptic genome diversity linked to pathogenicity

This project was funded by the UK Natural Environmental Research Council (NERC) grant NE/E006701/1, the European Research Council (ERC) grant 260801-BIG_IDEA, the Swiss National Science Foundation grant 31-125099 and the Biodiversa project RACE: Risk Assessment of Chytridiomycosis to European Amphibian Biodiversity (http://www.bd-maps.eu). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Peer reviewedPublisher PD

Microevolutionary traits and comparative population genomics of the emerging pathogenic fungus Cryptococcus gattii

Emerging fungal pathogens cause an expanding burden of disease across the animal kingdom, including a rise in morbidity and mortality in humans. Yet, we currently have only a limited repertoire of available therapeutic interventions. A greater understanding of the mechanisms of fungal virulence and of the emergence of hypervirulence within species is therefore needed for new treatments and mitigation efforts. For example, over the past decade, an unusual lineage of Cryptococcus gattii, which was first detected on Vancouver Island, has spread to the Canadian mainland and the Pacific Northwest infecting otherwise healthy individuals. The molecular changes that led to the development of this hypervirulent cryptococcal lineage remain unclear. To explore this, we traced the history of similar microevolutionary events that can lead to changes in host range and pathogenicity. Here, we detail fine-resolution mapping of genetic differences between two highly related Cryptococcus gattii VGIIc isolates that differ in their virulence traits (phagocytosis, vomocytosis, macrophage death, mitochondrial tubularization and intracellular proliferation). We identified a small number of single site variants within coding regions that potentially contribute to variations in virulence. We then extended our methods across multiple lineages of C. gattii to study how selection is acting on key virulence genes within different lineages. This article is part of the themed issue ‘Tackling emerging fungal threats to animal health, food security and ecosystem resilience’

Intercomparison of SCIAMACHY and OMI Tropospheric NO2 Columns: Observing the Diurnal Evolution of Chemistry and Emissions from Space

Concurrent (August 2006) measurements of tropospheric NO2 columns from OMI aboard Aura (1330 local overpass time) and SCIAMACHY aboard Envisat (1000 local overpass time) offer an opportunity to examine the consistency between the two instruments under tropospheric background conditions and the effect of different observing times. For scenes with tropospheric NO2 columns <5.0 × 1015 molecules cm−2, SCIAMACHY and OMI agree within 1.0–2.0 × 1015 molecules cm−2, consistent with the detection limits of both instruments. We find evidence for a low bias of 0.2 × 1015 molecules cm−2 in OMI observations over remote oceans. Over the fossil fuel source regions at northern midlatitudes, we find that SCIAMACHY observes up to 40% higher NO2 at 1000 local time (LT) than OMI at 1330 LT. Over biomass burning regions in the tropics, SCIAMACHY observes up to 40% lower NO2 columns than OMI. These differences are present in the spectral fitting of the data (slant column) and are augmented in the fossil fuel regions and dampened in the tropical biomass burning regions by the expected increase in air mass factor as the mixing depth rises from 1000 to 1330 LT. Using a global 3-D chemical transport model (GEOS-Chem), we show that the 1000–1330 LT decrease in tropospheric NO2 column over fossil fuel source regions can be explained by photochemical loss, dampened by the diurnal cycle of anthropogenic emissions that has a broad daytime maximum. The observed 1000–1330 LT NO2 column increase over tropical biomass burning regions points to a sharp midday peak in emissions and is consistent with a diurnal cycle of emissions derived from geostationary satellite fire counts.Earth and Planetary SciencesEngineering and Applied Science

External quantum efficiency measurements used to study the stability of differently deposited perovskite solar cells

The instability exhibited by perovskite solar cells when exposed to the environment under illumination is one major obstacle for the entry of perovskite technology on the photovoltaic market. In this work, we use the external quantum efficiency (EQE) technique to study the photoinduced degradation of two types of solar cells having CH3NH3PbI3 as absorber layer, one deposited by spin coating with an n-i-p architecture, and the other deposited by evaporation with an inverted p-i-n structure. We also study the effect of different encapsulants to protect the cells against atmospheric agents. We find that EQE provides information regarding the areas of the cell most susceptible to degradation, in addition to providing an estimate of the optical gap and the Urbach energy of the absorbent material. We confirm that the combined action of illumination and the environment markedly accelerate the degradation, which is reflected in the deterioration of all the parameters of the cell. The rear part of the cell is the first region to suffer the light-induced degradation. On the other hand, the cells deposited by evaporation and with a good encapsulation process are highly stable, since after 30 hours of exposure just small spectral change is noticed in the red/infrared region of the EQE spectrum

Common Reservoirs for Penicillium marneffei Infection in Humans and Rodents, China

Human penicilliosis marneffei is an emerging infectious disease caused by the fungus Penicillium marneffei. High prevalence of infection among bamboo rats of the genera Rhizomys and Cannomys suggest that these rodents are a key facet of the P. marneffei life cycle. We trapped bamboo rats during June 2004–July 2005 across Guangxi Province, China, and demonstrated 100% prevalence of infection. Multilocus genotypes show that P. marneffei isolates from humans are similar to those infecting rats and are in some cases identical. Comparison of our dataset with genotypes recovered from sites across Southeast Asia shows that the overriding component of genetic structure in P. marneffei is spatial, with humans containing a greater diversity of genotypes than rodents. Humans and bamboo rats are sampling an as-yet undiscovered common reservoir of infection, or bamboo rats are a vector for human infections by acting as amplifiers of infectious dispersal stages

Lipid production through the single-step microwave hydrolysis of macroalgae using the oleaginous yeast Metschnikowia pulcherrima

Macroalgae (seaweeds) represent an emerging resource for food and the production of commodity and specialty chemicals. In this study, a single-step microwave process was used to depolymerise a range of macroalgae native to the United Kingdom, producing a growth medium suitable for microbial fermentation. The medium contained a range of mono- and polysaccharides as well as macro- and micronutrients that could be metabolised by the oleaginous yeast Metschnikowia pulcherrima. Among twelve macroalgae species, the brown seaweeds exhibited the highest fermentation potential, especially the kelp Saccharina latissima. Applying a portfolio of ten native M. pulcherrima strains, yeast growth kinetics, as well as production of lipids and 2-phenylethanol were examined, with productivity and growth rate being strain dependent. On the 2 L scale, 6.9 g L−1 yeast biomass – a yield of 0.14 g g−1 with respect to the supplied macroalgae – containing 37.2% (w/w) lipid was achieved through utilisation of the proteins, mono- and polysaccharides from S. latissima, with no additional enzymes. In addition, the yeast degraded a range of fermentation inhibitors released upon microwave processing at high temperatures and long holding times. As macroalgae can be cultured to food grade, this system offers a novel, potentially low-cost route to edible microbial oils as well as a renewable feedstock for oleochemicals

Standardizing CYP2D6 Genotype to Phenotype Translation: Consensus Recommendations from the Clinical Pharmacogenetics Implementation Consortium and Dutch Pharmacogenetics Working Group

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/153095/1/cts12692_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/153095/2/cts12692-sup-0001-Supinfo.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/153095/3/cts12692.pd