Reentrant phase behaviour for systems with competition between phase separation and self-assembly

In patchy particle systems where there is competition between the self-assembly of finite clusters and liquid-vapour phase separation, reentrant phase behaviour is observed, with the system passing from a monomeric vapour phase to a region of liquid-vapour phase coexistence and then to a vapour phase of clusters as the temperature is decreased at constant density. Here, we present a classical statistical mechanical approach to the determination of the complete phase diagram of such a system. We model the system as a van der Waals fluid, but one where the monomers can assemble into monodisperse clusters that have no attractive interactions with any of the other species. The resulting phase diagrams show a clear region of reentrance. However, for the most physically reasonable parameter values of the model, this behaviour is restricted to a certain range of density, with phase separation still persisting at high densities.Comment: 13 pages, 10 figure

Multiplex meta-analysis of RNA expression to identify genes with variants associated with immune dysfunction

ObjectiveWe demonstrate a genome-wide method for the integration of many studies of gene expression of phenotypically similar disease processes, a method of multiplex meta-analysis. We use immune dysfunction as an example disease process.DesignWe use a heterogeneous collection of datasets across human and mice samples from a range of tissues and different forms of immunodeficiency. We developed a method integrating Tibshirani's modified t-test (SAM) is used to interrogate differential expression within a study and Fisher's method for omnibus meta-analysis to identify differentially expressed genes across studies. The ability of this overall gene expression profile to prioritize disease associated genes is evaluated by comparing against the results of a recent genome wide association study for common variable immunodeficiency (CVID).ResultsOur approach is able to prioritize genes associated with immunodeficiency in general (area under the ROC curve = 0.713) and CVID in particular (area under the ROC curve = 0.643).ConclusionsThis approach may be used to investigate a larger range of failures of the immune system. Our method may be extended to other disease processes, using RNA levels to prioritize genes likely to contain disease associated DNA variants

Thin, fine and with sensitivity: a metamethodology of intuitions

Do philosophers use intuitions? Should philosophers use intuitions? Can philosophical methods (where intuitions are concerned) be improved upon? In order to answer these questions we need to have some idea of how we should go about answering them. I defend a way of going about methodology of intuitions: a metamethodology. I claim the following: (i) we should approach methodological questions about intuitions with a thin conception of intuitions in mind; (ii) we should carve intuitions finely; and, (iii) we should carve to a grain to which we are sensitive in our everyday philosophising. The reason is that, unless we do so, we don’t get what we want from philosophical methodology. I argue that what we want is information that will aid us in formulating practical advice concerning how to do philosophy responsibly/well/better

Identification of dfrA14 in two distinct plasmids conferring trimethoprim resistance in Actinobacillus pleuropneumoniae

OBJECTIVES: The objective of this study was to determine the distribution and genetic basis of trimethoprim resistance in Actinobacillus pleuropneumoniae isolates from pigs in England. METHODS: Clinical isolates collected between 1998 and 2011 were tested for resistance to trimethoprim and sulphonamide. The genetic basis of trimethoprim resistance was determined by shotgun WGS analysis and the subsequent isolation and sequencing of plasmids. RESULTS: A total of 16 (out of 106) A. pleuropneumoniae isolates were resistant to both trimethoprim (MIC >32 mg/L) and sulfisoxazole (MIC ≥256 mg/L), and a further 32 were resistant only to sulfisoxazole (MIC ≥256 mg/L). Genome sequence data for the trimethoprim-resistant isolates revealed the presence of the dfrA14 dihydrofolate reductase gene. The distribution of plasmid sequences in multiple contigs suggested the presence of two distinct dfrA14-containing plasmids in different isolates, which was confirmed by plasmid isolation and sequencing. Both plasmids encoded mobilization genes, the sulphonamide resistance gene sul2, as well as dfrA14 inserted into strA, a streptomycin-resistance-associated gene, although the gene order differed between the two plasmids. One of the plasmids further encoded the strB streptomycin-resistance-associated gene. CONCLUSIONS: This is the first description of mobilizable plasmids conferring trimethoprim resistance in A. pleuropneumoniae and, to our knowledge, the first report of dfrA14 in any member of the Pasteurellaceae. The identification of dfrA14 conferring trimethoprim resistance in A. pleuropneumoniae isolates will facilitate PCR screens for resistance to this important antimicrobial

Trafficking of prion proteins through a caveolae-mediated endosomal pathway

To understand the posttranslational conversion of the cellular prion protein (PrPC) to its pathologic conformation, it is important to define the intracellular trafficking pathway of PrPC within the endomembrane system. We studied the localization and internalization of PrPC in CHO cells using cryoimmunogold electron microscopy. At steady state, PrPC was enriched in caveolae both at the TGN and plasma membrane and in interconnecting chains of endocytic caveolae. Protein A–gold particles bound specifically to PrPC on live cells. These complexes were delivered via caveolae to the pericentriolar region and via nonclassical, caveolae-containing early endocytic structures to late endosomes/lysosomes, thereby bypassing the internalization pathway mediated by clathrin-coated vesicles. Endocytosed PrPC-containing caveolae were not directed to the ER and Golgi complex. Uptake of caveolae and degradation of PrPC was slow and sensitive to filipin. This caveolae-dependent endocytic pathway was not observed for several other glycosylphosphatidyl inositol (GPI)-anchored proteins. We propose that this nonclassical endocytic pathway is likely to determine the subcellular location of PrPC conversion

Do we need to rethink our waterways? Values of ageing waterways in current and future society

In the past canals were developed, and some rivers were heavily altered, driven by the need for good transportation infrastructure. Major investments were made in navigation locks, weirs and artificial embankments, and many of these assets are now reaching the end of their technical lifetime. Since then the concept of integrated water resource management (IWRM) emerged as a concept to manage and develop water-bodies in general. Two pressing problems arise from these developments: (1) major reinvestment is needed in order to maintain the transportation function of these waterways, and (2), it is not clear how the implementation of the concept of IWRM can be brought into harmony with such reinvestment. This paper aims to illustrate the problems in capital-intensive parts of waterway systems, and argues for exploring value-driven solutions that rely on the inclusion of multiple values, thus solving both funding problems and stakeholder conflicts. The focus on value in cooperative strategies is key to defining viable implementation strategies for waterway projects

Alpine glacier algal bloom during a record melt year

Glacier algal blooms dominate the surfaces of glaciers and ice sheets during summer melt seasons, with larger blooms anticipated in years that experience the greatest melt. Here, we characterize the glacier algal bloom proliferating on Morteratsch glacier, Switzerland, during the record 2022 melt season, when the Swiss Alps lost three times more ice than the decadal average. Glacier algal cellular abundance (cells ml−1), biovolume (μm3 cell−1), photophysiology (Fv/Fm, rETRmax), and stoichiometry (C:N ratios) were constrained across three elevations on Morteratsch glacier during late August 2022 and compared with measurements of aqueous geochemistry and outputs of nutrient spiking experiments. While a substantial glacier algal bloom was apparent during summer 2022, abundances ranged from 1.78 × 104 to 8.95 × 105 cells ml−1 of meltwater and did not scale linearly with the magnitude of the 2022 melt season. Instead, spatiotemporal heterogeneity in algal distribution across Morteratsch glacier leads us to propose melt-water-redistribution of (larger) glacier algal cells down-glacier and presumptive export of cells from the system as an important mechanism to set overall bloom carrying capacity on steep valley glaciers during high melt years. Despite the paradox of abundant glacier algae within seemingly oligotrophic surface ice, we found no evidence for inorganic nutrient limitation as an important bottom-up control within our study site, supporting our hypothesis above. Fundamental physical constraints may thus cap bloom carrying-capacities on valley glaciers as 21st century melting continues