The AMR problem: demanding economies, biological margins, and co-producing alternative strategies

 This is the final version. Available from Palgrave Macmillan via the DOI in this record.Widespread antimicrobial resistance (AMR) poses a threat to public and animal health, and has consequences for the structure and sustainability of food production. The problem is often framed as one of inappropriate antimicrobial use, which drives emergence and selection of resistant microbes. The answer to this framing of the problem is to lower disease incidence and transmission rates, regulate antimicrobial uses and to educate prescribers and users of medicines. In this paper we argue that this seemingly straightforward programme of action is beset by at least two difficulties. First, in many parts of the world, disease dynamics and antimicrobial uses are embedded within biosocially demanding settings. Second, antibiotic use is one among many possible drivers of resistance. We focus on the aquatic environment and aquacultural food production where resistance drivers may relate to a variety of processes. Using interviews, survey data, and participatory modelling exercises with competency groups in Bangladesh’s shrimp and prawn aquaculture sector, we demonstrate the need to understand economic and biological drivers of disease, farmer adaptations to disease risks and the potential paradox of pursuing pathogen-free food production as a means to reduce AMR risks. We argue that the AMR problem needs to be framed as an adaptive rather than technical challenge, and involves ownership, change and experimentation across a range of relevant sites.Economic and Social Research Council (ESRC

Modeled Subglacial Water Flow Routing Supports Localized Intrusive Heating as a Possible Cause of Basal Melting of Mars' South Polar Ice Cap

The discovery of a ~20 km wide area of bright subsurface radar reflections, interpreted as liquid water, beneath the Martian south polar layered deposits (SPLD) in data from the Mars Advanced Radar for Subsurface and Ionosphere Sounding (MARSIS) instrument, and the discovery of two geologically recent potential eskers (landforms produced by subglacial melt) associated with viscous flow features in Martian mid-latitudes, has suggested recent basal melting of Martian ice deposits may be feasible, possibly due to locally elevated geothermal heating. Locations of terrestrial subglacial lakes and major drainage axes have been successfully predicted from subglacial hydraulic potential surfaces calculated from surface topography and ice thickness. Here, we use surface topography from the Mars Orbiter Laser Altimeter and SPLD bed elevations derived from MARSIS data to calculate the subglacial hydraulic potential surface beneath the SPLD and determine whether the observed high reflectance area coincides with predicted subglacial lake locations. Given the sensitivity of terrestrial predictions of lake locations to basal topography, we derive over 1000 perturbed topographies (using noise statistics from the MARSIS data) to infer the most likely locations of possible subglacial water bodies and drainage axes. Our results show that the high reflectance area does not coincide with any substantial predicted lake locations; three nearby lake locations are robustly predicted however. We interpret this result as suggesting that the high reflectance area (assuming the interpretation as liquid is correct) is most likely a hydraulically-isolated patch of liquid confined by the surrounding cold-based ice, rather than a topographically-constrained subglacial lake

Potassium availability triggers Mycobacterium tuberculosis transition to, and resuscitation from, non-culturable (dormant) states.

Dormancy in non-sporulating bacteria is an interesting and underexplored phenomenon with significant medical implications. In particular, latent tuberculosis may result from the maintenance of Mycobacterium tuberculosis bacilli in non-replicating states in infected individuals. Uniquely, growth of M. tuberculosis in aerobic conditions in potassium-deficient media resulted in the generation of bacilli that were non-culturable (NC) on solid media but detectable in liquid media. These bacilli were morphologically distinct and tolerant to cell-wall-targeting antimicrobials. Bacterial counts on solid media quickly recovered after washing and incubating bacilli in fresh resuscitation media containing potassium. This resuscitation of growth occurred too quickly to be attributed to M. tuberculosis replication. Transcriptomic and proteomic profiling through adaptation to, and resuscitation from, this NC state revealed a switch to anaerobic respiration and a shift to lipid and amino acid metabolism. High concordance with mRNA signatures derived from M. tuberculosis infection models suggests that analogous NC mycobacterial phenotypes may exist during disease and may represent unrecognized populations in vivo. Resuscitation of NC bacilli in potassium-sufficient media was characterized by time-dependent activation of metabolic pathways in a programmed series of processes that probably transit bacilli through challenging microenvironments during infection

Recent Basal Melting of a Mid-Latitude Glacier on Mars

Evidence for past basal melting of young (late Amazonian), debris-covered glaciers in Mars’ mid-latitudes is extremely rare. Thus, it is widely thought that these viscous flow features (VFFs) have been perennially frozen to their beds. We identify an instance of recent, localized wet-based mid-latitude glaciation, evidenced by a candidate esker emerging from a VFF in a tectonic rift in Tempe Terra. Eskers are sedimentary ridges deposited in ice-walled meltwater conduits and are indicative of glacial melting. We compare the candidate esker to terrestrial analogues, present a geomorphic map of landforms in the rift, and develop a landsystem model to explain their formation. We propose that the candidate esker formed during a transient phase of wet-based glaciation. We then consider the similarity between the geologic setting of the new candidate esker and that of the only other candidate esker to be identified in association with an existing mid-latitude VFF; both are within tectonic graben/rifts proximal to volcanic provinces. Finally, we calculate potential basal temperatures for a range of VFF thicknesses, driving stresses, mean annual surface temperatures, and geothermal heat fluxes, which unlike previous studies, include the possible role of internal strain heating. Strain heating can form an important additional heat source, especially in flow convergence zones, or where ice is warmer due to elevated surface temperatures or geothermal heat flux. Elevated geothermal heat flux within rifts, perhaps combined with locally-elevated strain heating, may have permitted wet-based glaciation during the late Amazonian, when cold climates precluded more extensive wet-based glaciation on Mars

Molecular Mechanisms of Membrane Deformation by I-BAR Domain Proteins

Conclusions: These data define I-BAR domain as a functional member of the BAR domain superfamily and unravel the mechanisms by which I-BAR domains deform membranes to induce filopodia in cells. Furthermore, our work reveals unexpected divergence in the mechanisms by which evolutionarily distinct groups of I-BAR domains interact with PI(4,5)P(2)-rich membranes

Gaseous carbonation of cementitious backfill for geological disposal of radioactive waste: Nirex Reference Vault Backfill

The ability of Nirex Reference Vault Backfill (NRVB), a cement backfill material, to capture carbon dioxide from Intermediate Level Radioactive waste packages after repository backfilling, has been assessed. Large-scale trials assessed the physical and chemical reaction of carbon dioxide with the hardened backfill grout. A carbonation front, radial in nature, was observed extending into the grout and three distinct regions were identified in the hardened grouts. A carbonated region, a carbonation front, and a partially carbonated zone were discerned. Potassium, and to a lesser extent sodium, were concentrated in the carbonated region just behind of the main reaction front. The area just ahead of the carbonation front was enriched in both sulphur and aluminium, while sulphur was found to be depleted from the carbonated material behind the main reaction front. Within the main carbonated region, virtually all of the hydrated cement phases were found to be carbonated, and carbonation extended throughout the grout, even within material indicated by phenolphthalein solution to be uncarbonated. Importantly, carbonation was observed to impact both the mineral assemblage and porosity of the cement backfill; it is therefore important to understand these characteristics in terms of the long term evolution of NRVB and its groundwater buffering safety function within the geological disposal facility near-field

Progress in human picornavirus research: New findings from the AIROPico consortium

Several research groups in Europe are active on different aspects of human picornavirus research. The AIROPico (Academia-Industry R&D Opportunities for Picornaviruses) consortium combined the disciplines of pathogenesis, diagnostics and therapy development in order to fill the gaps in our understanding of how picornaviruses cause human disease and how to combat them. AIROPico was the first EU consortium dedicated to human picornavirus research and development, and has largely accelerated and improved R&D on picornavirus biology, diagnostics and therapy. In this article, we present the progress on pathogenesis, diagnostics and treatment strategy developments for human picornaviruses resulting from the structured, translational research approach of the AIROPico consortium. We here summarize new insights in protection against infection by maternal or cross-protective antibodies, the visualisation of interactions between virus and neutralizing antibodies by cryoEM structural imaging, and the outcomes from a picornavirus-infected human 3D organoid. Progress in molecular detection and a fast typing assay for rhinovirus species are presented, as well as the identification of new compounds potentially interesting as therapeutic compounds.</p

Validation of pooled genotyping on the Affymetrix 500 k and SNP6.0 genotyping platforms using the polynomial-based probe-specific correction

10.1186/1471-2156-10-82BMC Genetics10-BGME

Three-Dimensional Structure of the Enveloped Bacteriophage Φ12: An Incomplete T = 13 Lattice Is Superposed on an Enclosed T = 1 Shell

BACKGROUND:Bacteriophage phi12 is a member of the Cystoviridae, a unique group of lipid containing membrane enveloped bacteriophages that infect the bacterial plant pathogen Pseudomonas syringae pv. phaseolicola. The genomes of the virus species contain three double-stranded (dsRNA) segments, and the virus capsid itself is organized in multiple protein shells. The segmented dsRNA genome, the multi-layered arrangement of the capsid and the overall viral replication scheme make the Cystoviridae similar to the Reoviridae. METHODOLOGY/PRINCIPAL FINDINGS:We present structural studies of cystovirus phi12 obtained using cryo-electron microscopy and image processing techniques. We have collected images of isolated phi12 virions and generated reconstructions of both the entire particles and the polymerase complex (PC). We find that in the nucleocapsid (NC), the phi12 P8 protein is organized on an incomplete T = 13 icosahedral lattice where the symmetry axes of the T = 13 layer and the enclosed T = 1 layer of the PC superpose. This is the same general protein-component organization found in phi6 NC's but the detailed structure of the entire phi12 P8 layer is distinct from that found in the best classified cystovirus species phi6. In the reconstruction of the NC, the P8 layer includes protein density surrounding the hexamers of P4 that sit at the 5-fold vertices of the icosahedral lattice. We believe these novel features correspond to dimers of protein P7. CONCLUSIONS/SIGNIFICANCE:In conclusion, we have determined that the phi12 NC surface is composed of an incomplete T = 13 P8 layer forming a net-like configuration. The significance of this finding in regard to cystovirus assembly is that vacancies in the lattice could have the potential to accommodate additional viral proteins that are required for RNA packaging and synthesis