A structural comparison of models of colloid-polymer mixtures

We study the structure of colloidal fluids with reference to colloid-polymer mixtures. We compare the one component description of the Asakura-Oosawa (AO) idealisation of colloid-polymer mixtures with the full two-component model. We also consider the Morse potential, a variable range interaction, for which the ground state clusters are known. Mapping the state points between these systems, we find that the pair structure of the full AO model is equally well described by the Morse potential or the one component AO approach. We employ a recently developed method to identify in the bulk fluid the ground state clusters relevant to the Morse potential. Surprisingly, when we measure the cluster populations, we find that the Morse fluid is significantly closer the full AO fluid than the one component AO description.Comment: 13 pages, accepted by J. Phys. Condens: Matter special issue for CECAM meeting 'New Trends in Simulating Colloids: from Models to Applications

The effect of attractions on the local structure of liquids and colloidal fluids

We revisit the role of attractions in liquids and apply these concepts to colloidal suspensions. Two means are used to investigate the structure; the pair correlation function and a recently developed topological method. The latter identifies structures topologically equivalent to ground state clusters formed by isolated groups of 5 < m < 13 particles, which are specific to the system under consideration. Our topological methodology shows that, in the case of Lennard-Jones, the addition of attractions increases the system's ability to form larger (m>8) clusters, although pair-correlation functions are almost identical. Conversely, in the case of short-ranged attractions, pair correlation functions show a significant response to adding attraction, while the liquid structure exhibits a strong decrease in clustering upon adding attractions. Finally, a compressed, weakly interacting system shows a similar pair structure and topology.Comment: 22 page

The development of a mouse model to explore resistance and susceptibility to early Ascaris suum infection

Ascaris suum and Ascaris lumbricoides exhibit an over-dispersed frequency distribution in their host populations in both the adult and larval stages. The impact of host factors on this observed distribution is still poorly understood and difficult to investigate in the natural host populations. The use of a mouse model has been supported by the observations that the larval migratory pattern, in this host, mimics the pattern observed in the pig. We explored the extrinsic factors that might affect the quantitative recovery of larvae during this migration in order to standardize a model system facilitating accurate future assessment of host genetic variation on this phase of the infection. In Exp. 1 larvae accumulated in the livers of both C57BL/6j and BALB/c mice up to and including days 4–5 p.i. and then declined in both strains until day 9. Loss of larvae from the livers corresponded to arrival in the lungs and maximum accumulation on day 7 p.i. but recovery was considerably higher in C57BL/6j mice. It was concluded that day 7 recoveries gave the best indication of relative resistance/susceptibility to this parasite. In Exp. 2 A/J, BALB/c, CBA/Ca, C57BL/6j, C3H/HeN, DBA/2, NIH, SJL, and SWR mice were compared. C57BL/6j mice were identified as the most susceptible strain and CBA/Ca mice as having the most contrasting phenotype, but with a similar kinetic pattern of migration. Finally, in Exp. 3, a strong positive correlation between the size of the inoculum and the mean worm recovery from the lungs was found in CBA/Ca and C57BL/6j mice, but the difference between these strains was highly consistent, 66.6–80%, regardless of the initial dose. These results demonstrate that, using our protocols for infection and recovery, between-experiment variation in A. suum worm burdens is minimal, and that C57BL/6j mice are highly susceptible to infection compared to other strains. The mechanistic basis of this susceptibility in relation to the resistance of other strains is unknown, but the possibilities are reviewed

Structure and kinetics in the freezing of nearly hard spheres

We consider homogeneous crystallisation rates in confocal microscopy experiments on colloidal nearly hard spheres at the single particle level. These we compare with Brownian dynamics simuations by carefully modelling the softness in the interactions with a Yukawa potential, which takes account of the electrostatic charges present in the experimental system. Both structure and dynamics of the colloidal fluid are very well matched between experiment and simulation, so we have confidence that the system simulated is close to that in the experiment. In the regimes we can access, we find reasonable agreement in crystallisation rates between experiment and simulations, noting that the larger system size in experiments enables the formation of critical nuclei and hence crystallisation at lower supersaturations than the simulations. We further examine the structure of the metastable fluid with a novel structural analysis, the topological cluster classification. We find that at densities where the hard sphere fluid becomes metastable, the dominant structure is a cluster of m=10 particles with five-fold symmetry. At a particle level, we find three regimes for the crystallisation process: metastable fluid (dominated by m=10 clusters), crystal and a transition region of frequent hopping between crystal-like environments and other (m\neq10) structuresComment: 10 page

Ionic immune suppression within the tumour microenvironment limits T cell effector function.

Tumours progress despite being infiltrated by tumour-specific effector T cells. Tumours contain areas of cellular necrosis, which are associated with poor survival in a variety of cancers. Here, we show that necrosis releases intracellular potassium ions into the extracellular fluid of mouse and human tumours, causing profound suppression of T cell effector function. Elevation of the extracellular potassium concentration ([K+]e) impairs T cell receptor (TCR)-driven Akt-mTOR phosphorylation and effector programmes. Potassium-mediated suppression of Akt-mTOR signalling and T cell function is dependent upon the activity of the serine/threonine phosphatase PP2A. Although the suppressive effect mediated by elevated [K+]e is independent of changes in plasma membrane potential (Vm), it requires an increase in intracellular potassium ([K+]i). Accordingly, augmenting potassium efflux in tumour-specific T cells by overexpressing the potassium channel Kv1.3 lowers [K+]i and improves effector functions in vitro and in vivo and enhances tumour clearance and survival in melanoma-bearing mice. These results uncover an ionic checkpoint that blocks T cell function in tumours and identify potential new strategies for cancer immunotherapy

Pollen, biomarker and stable isotope evidence of late Quaternary environmental change at Lake McKenzie, southeast Queensland

Unravelling links between climate change and vegetation response during the Quaternary is important if the climate–environment interactions of modern systems are to be fully understood. Using a sediment core from Lake McKenzie, Fraser Island, we reconstruct changes in the lake ecosystem and surrounding vegetation over the last ca. 36.9 cal kyr. Evidence is drawn from multiple sources, including pollen, micro-charcoal, biomarker and stable isotope (C and N) analyses, and is used to gain a better understanding of the nature and timing of past ecological changes that have occurred at the site. The glacial period of the record, from ca. 36.9 to 18.3 cal kyr BP, is characterised by an increased abundance of plants of the aquatic and littoral zone, indicating lower lake water levels. High abundance of biomarkers and microfossils of the colonial green alga Botryococcus occurred at this time and included large variation in individual botryococcene d13C values. A slowing or ceasing of sediment accumulation occurred during the time period from ca. 18.3 to 14.0 cal kyr BP. By around 14.0 cal kyr BP fire activity in the area was reduced, as was abundance of littoral plants and terrestrial herbs, suggesting wetter conditions from that time. The Lake McKenzie pollen record conforms to existing records from Fraser Island by containing evidence of a period of reduced effective precipitation that commenced in the mid-Holocene

OptCom: A Multi-Level Optimization Framework for the Metabolic Modeling and Analysis of Microbial Communities

Microorganisms rarely live isolated in their natural environments but rather function in consolidated and socializing communities. Despite the growing availability of high-throughput sequencing and metagenomic data, we still know very little about the metabolic contributions of individual microbial players within an ecological niche and the extent and directionality of interactions among them. This calls for development of efficient modeling frameworks to shed light on less understood aspects of metabolism in microbial communities. Here, we introduce OptCom, a comprehensive flux balance analysis framework for microbial communities, which relies on a multi-level and multi-objective optimization formulation to properly describe trade-offs between individual vs. community level fitness criteria. In contrast to earlier approaches that rely on a single objective function, here, we consider species-level fitness criteria for the inner problems while relying on community-level objective maximization for the outer problem. OptCom is general enough to capture any type of interactions (positive, negative or combinations thereof) and is capable of accommodating any number of microbial species (or guilds) involved. We applied OptCom to quantify the syntrophic association in a well-characterized two-species microbial system, assess the level of sub-optimal growth in phototrophic microbial mats, and elucidate the extent and direction of inter-species metabolite and electron transfer in a model microbial community. We also used OptCom to examine addition of a new member to an existing community. Our study demonstrates the importance of trade-offs between species- and community-level fitness driving forces and lays the foundation for metabolic-driven analysis of various types of interactions in multi-species microbial systems using genome-scale metabolic models