Partitioning of fungal assemblages across different marine habitats

© 2016 Society for Applied Microbiology and John Wiley & Sons Ltd. Fungi are a highly diverse group of microbes that fundamentally influence the biogeochemistry of the biosphere, but we currently know little about the diversity and distribution of fungi in aquatic habitats. Here we describe shifts in marine fungal community composition across different marine habitats, using targeted pyrosequencing of the fungal Internal Transcribed Spacer (ITS) region. Our results demonstrate strong partitioning of fungal community composition between estuarine, coastal and oceanic samples, with each habitat hosting discrete communities that are controlled by patterns in salinity, temperature, oxygen and nutrients. Whereas estuarine habitats comprised a significant proportion of fungal groups often found in terrestrial habitats, the open ocean sites were dominated by previously unidentified groups. The patterns observed here indicate that fungi are potentially a significant, although largely overlooked, feature of the ocean's microbiota, but greater efforts to characterize marine species are required before the full ecological and biogeochemical importance of marine fungi can be ascertained

Multi-Method Characterisation of the Human Circulating Microbiome

The term microbiome describes the genetic material encoding the various microbial populations that inhabit our body. Whilst colonization of various body niches (e.g., the gut) by dynamic communities of microorganisms is now universally accepted, the existence of microbial populations in other “classically sterile” locations, including the blood, is a relatively new concept. The presence of bacteria-specific DNA in the blood has been reported in the literature for some time, yet the true origin of this is still the subject of much deliberation. The aim of this study was to investigate the phenomenon of a “blood microbiome” by providing a comprehensive description of bacterially derived nucleic acids using a range of complementary molecular and classical microbiological techniques. For this purpose we utilized a set of plasma samples from healthy subjects (n = 5) and asthmatic subjects (n = 5). DNA-level analyses involved the amplification and sequencing of the 16S rRNA gene. RNA-level analyses were based upon the de novo assembly of unmapped mRNA reads and subsequent taxonomic identification. Molecular studies were complemented by viability data from classical aerobic and anaerobic microbial culture experiments. At the phylum level, the blood microbiome was predominated by Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes. The key phyla detected were consistent irrespective of molecular method (DNA vs. RNA), and consistent with the results of other published studies. In silico comparison of our data with that of the Human Microbiome Project revealed that members of the blood microbiome were most likely to have originated from the oral or skin communities. To our surprise, aerobic and anaerobic cultures were positive in eight of out the ten donor samples investigated, and we reflect upon their source. Our data provide further evidence of a core blood microbiome, and provide insight into the potential source of the bacterial DNA/RNA detected in the blood. Further, data reveal the importance of robust experimental procedures, and identify areas for future consideration

Multi-Method Characterisation of the Human Circulating Microbiome

The term microbiome describes the genetic material encoding the various microbial populations that inhabit our body. Whilst colonization of various body niches (e.g., the gut) by dynamic communities of microorganisms is now universally accepted, the existence of microbial populations in other “classically sterile” locations, including the blood, is a relatively new concept. The presence of bacteria-specific DNA in the blood has been reported in the literature for some time, yet the true origin of this is still the subject of much deliberation. The aim of this study was to investigate the phenomenon of a “blood microbiome” by providing a comprehensive description of bacterially derived nucleic acids using a range of complementary molecular and classical microbiological techniques. For this purpose we utilized a set of plasma samples from healthy subjects (n = 5) and asthmatic subjects (n = 5). DNA-level analyses involved the amplification and sequencing of the 16S rRNA gene. RNA-level analyses were based upon the de novo assembly of unmapped mRNA reads and subsequent taxonomic identification. Molecular studies were complemented by viability data from classical aerobic and anaerobic microbial culture experiments. At the phylum level, the blood microbiome was predominated by Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes. The key phyla detected were consistent irrespective of molecular method (DNA vs. RNA), and consistent with the results of other published studies. In silico comparison of our data with that of the Human Microbiome Project revealed that members of the blood microbiome were most likely to have originated from the oral or skin communities. To our surprise, aerobic and anaerobic cultures were positive in eight of out the ten donor samples investigated, and we reflect upon their source. Our data provide further evidence of a core blood microbiome, and provide insight into the potential source of the bacterial DNA/RNA detected in the blood. Further, data reveal the importance of robust experimental procedures, and identify areas for future consideration

Organising care, practice and participative research : Papers from the cognitive decline partnership centre

Non peer reviewe

Linking urban aerosol fluxes in street canyons to larger scale emissions

In this study we investigate ultrafine particle (UFP) fluxes using a first order eddy viscosity turbulence closure Computational Fluid Dynamics (CFD) model and determine the different factors that influence emissions of UFP into the urban boundary layer. Both vertical turbulent fluxes as well as the fluxes due to mean circulatory flow are shown to contribute to the overall ventilation characteristics of street canyons. We then derive a simple parameterised numerical prediction model for canyon top UFP venting which is then compared with tower based micrometeorological flux measurements obtained during the REPARTEE & CityFlux field experiments

Truncated and Helix-Constrained Peptides with High Affinity and Specificity for the cFos Coiled-Coil of AP-1

Protein-based therapeutics feature large interacting surfaces. Protein folding endows structural stability to localised surface epitopes, imparting high affinity and target specificity upon interactions with binding partners. However, short synthetic peptides with sequences corresponding to such protein epitopes are unstructured in water and promiscuously bind to proteins with low affinity and specificity. Here we combine structural stability and target specificity of proteins, with low cost and rapid synthesis of small molecules, towards meeting the significant challenge of binding coiled coil proteins in transcriptional regulation. By iteratively truncating a Jun-based peptide from 37 to 22 residues, strategically incorporating i-->i+4 helix-inducing constraints, and positioning unnatural amino acids, we have produced short, water-stable, alpha-helical peptides that bind cFos. A three-dimensional NMR-derived structure for one peptide (24) confirmed a highly stable alpha-helix which was resistant to proteolytic degradation in serum. These short structured peptides are entropically pre-organized for binding with high affinity and specificity to cFos, a key component of the oncogenic transcriptional regulator Activator Protein-1 (AP-1). They competitively antagonized the cJun–cFos coiled-coil interaction. Truncating a Jun-based peptide from 37 to 22 residues decreased the binding enthalpy for cJun by ~9 kcal/mol, but this was compensated by increased conformational entropy (TDS ≤ 7.5 kcal/mol). This study demonstrates that rational design of short peptides constrained by alpha-helical cyclic pentapeptide modules is able to retain parental high helicity, as well as high affinity and specificity for cFos. These are important steps towards small antagonists of the cJun-cFos interaction that mediates gene transcription in cancer and inflammatory diseases

Plutonium transfer to wildlife at legacy sites

When internalized within an organism’s body, plutonium (Pu) can be important in dose calculation due to its relatively high-energy alpha emissions (~5-6 MeV). In this paper we quantify transfer of Pu to a range of wildlife types at legacy nuclear weapons sites and evaluate the importance of body tissue Pu distribution in the transfer of Pu through the food chain. The paper presents new data from Maralinga, Australia, as well as past data from terrestrial and marine settings of the US nuclear research program

Atmospheric distribution of HCN from satellite observations and 3-D model simulations

Hydrogen cyanide (HCN) is an important tracer of biomass burning, but there are significant uncertainties in its atmospheric budget, especially its photochemical and ocean sinks. Here we use a tracer version of the TOMCAT global 3-D chemical transport model to investigate the physical and chemical processes driving the abundance of HCN in the troposphere and stratosphere over the period 2004–2016. The modelled HCN distribution is compared with version 4.1 of the Atmospheric Chemistry Experiment Fourier transform spectrometer (ACE-FTS) HCN satellite data, which provide profiles up to around 42 km, and with ground-based column measurements from the Network for the Detection of Atmospheric Composition Change (NDACC). The long-term ACE-FTS measurements reveal the strong enhancements in upper-tropospheric HCN due to large wildfire events in Indonesia in 2006 and 2015. Our 3-D model simulations confirm previous lower-altitude balloon comparisons that the currently recommended NASA Jet Propulsion Laboratory (JPL) reaction rate coefficient of HCN with OH greatly overestimates the HCN loss. The use of the rate coefficient proposed by Kleinböhl et al. (2006) in combination with the HCN oxidation by O(1D) gives good agreement between ACE-FTS observations and the model. Furthermore, the model photochemical loss terms show that the reduction in the HCN mixing ratio with height in the middle stratosphere is mainly driven by the O(1D) sink with only a small contribution from a reaction with OH. From comparisons of the model tracers with ground-based HCN observations we test the magnitude of the ocean sink in two different published schemes (Li et al., 2000, 2003). We find that in our 3-D model the two schemes produce HCN abundances which are very different to the NDACC observations but in different directions. A model HCN tracer using the Li et al. (2000) scheme overestimates the HCN concentration by almost a factor of 2, while a HCN tracer using the Li et al. (2003) scheme underestimates the observations by about one-third. To obtain good agreement between the model and observations, we need to scale the magnitudes of the global ocean sinks by factors of 0.25 and 2 for the schemes of Li et al. (2000) and Li et al. (2003), respectively. This work shows that the atmospheric photochemical sinks of HCN now appear well constrained but improvements are needed in parameterizing the major ocean uptake sink

Impact of the June 2018 Saddleworth Moor wildfires on air quality in northern England

The June 2018 Saddleworth Moor fires were some of the largest UK wildfires on record and lasted for approximately three weeks. They emitted large quantities of smoke, trace gases and aerosols which were transported downwind over the highly populated regions of Manchester and Liverpool. Surface observations of PM2.5 indicate that concentrations were 4–5.5 times higher than the recent seasonal average. State-of-the-art satellite measurements of total column carbon monoxide (TCCO) from the TROPOMI instrument on the Sentinel 5—Precursor (S5P) platform, coupled with measurements from a flight of the UK BAe-146–301 research aircraft, are used to quantify the substantial enhancement in emitted trace gases. The aircraft measured plume enhancements with near-fire CO and PM2.5 concentrations >1500 ppbv and >125 μg m−3 (compared to ~100 ppbv and ~5 μg m−3 background concentrations). Downwind fire-plume ozone (O3) values were larger than the near-fire location, indicating O3 production with distance from source. The near-fire O3:CO ratio was (ΔO3/ΔCO) 0.001 ppbv/ppbv, increasing downwind to 0.060–0.105 ppbv/ppbv, suggestive of O3 production enhancement downwind of the fires. Emission rates of CO and CO2 ranged between 1.07 (0.07–4.69) kg s−1 and 13.7 (1.73–50.1) kg s−1, respectively, similar to values expected from a medium sized power station

Unusual tumours of the heart: diagnostic and prognostic implications

Metastases to the heart are extremely uncommon. We describe three unusual cases along with their management. A review of the current literature concerning cardiac secondaries is included