Structural and biophysical characterisation of Escherichia coli alpha-2-macroglobulin and its interaction with penicillin binding protein 1C

The alpha-2-macroglobulin superfamily consists of large multi-domain proteins that are activated by protease cleavage. One arm of this family consists of protease inhibitors that undergo a large conformational change upon protease cleavage, simultaneously physically trapping the cleaving protease and covalently linking to it via a thioester bond. However, there is little mechanistic understanding of how protease cleavage activates the conformational changes that lead to protease inactivation. These protease inhibitors are found in tetrameric, dimeric and monomer forms within eukaryotic blood/lymph fluid. The recently described Escherichia coli alpha-2-macroglobulin (ECAM) is a periplasmic, inner membrane anchored protease inhibitor. The gene encoding ECAM, yfhM, is found within an operon alongside pbpC, which encodes penicillin binding protein 1C. These two proteins have been proposed to function in defence and repair against host proteases with ECAM acting to inhibit proteases that have breached the outer membrane and Pbp1C repairing damage to the peptide linkages within the peptidoglycan layer. This thesis describes the structural and biophysical characterisation of ECAM and an investigation into the role of Pbp1C in ECAM function. In order to gain insight into the mechanism through which protease cleavage activates ECAM we used a combination of X-ray crystallography, small angle X-ray scattering and analytical ultracentrifugation to characterise the conformational changes that occur on protease cleavage. The X-ray structure of protease cleaved ECAM revealed a putative mechanism of activation and conformational change essential for protease inhibition. In this competitive mechanism, protease cleavage of the bait-region domain results in the untethering of an intrinsically disordered region of this domain which disrupts native inter-domain interactions that maintain ECAM in the inactivated form. Owing to the similarity in structure and domain architecture of ECAM and human α-2-macroglobulin, this protease-activation mechanism is likely to operate across the diverse members of this group. Further to this, it was shown that ECAM is processed in vivo, existing largely as truncated forms in growing E. coli cells. Interestingly, Pbp1C plays a key role in ECAM processing, with cell lacking pbpC showing an accumulation of full-length and dimeric forms of ECAM

The ubiK protein is an accessory factor necessary for bacterial Ubiquinone (UQ) biosynthesis and forms a complex with the UQ biogenesis factor UbiJ

Ubiquinone (UQ), also referred to as coenzyme Q, is a widespread lipophilic molecule in both prokaryotes and eukaryotes in which it primarily acts as an electron carrier. Eleven proteins are known to participate in UQ biosynthesis in Escherichia coli, and we recently demonstrated that UQ biosynthesis requires additional, nonenzymatic factors, some of which are still unknown. Here, we report on the identification of a bacterial gene, yqiC, which is required for efficient UQ biosynthesis, and which we have renamed ubiK. Using several methods, we demonstrated that the UbiK protein forms a complex with the C-terminal part of UbiJ, another UQ biogenesis factor we previously identified. We found that both proteins are likely to contribute to global UQ biosynthesis rather than to a specific biosynthetic step, because both ubiK and ubiJ mutants accumulated octaprenylphenol, an early intermediate of the UQ biosynthetic pathway. Interestingly, we found that both proteins are dispensable for UQ biosynthesis under anaerobiosis, even though they were expressed in the absence of oxygen. We also provide evidence that the UbiK-UbiJ complex interacts with palmitoleic acid, a major lipid in E. coli. Last, in Salmonella enterica, ubiK was required for proliferation in macrophages and virulence in mice. We conclude that although the role of the UbiK-UbiJ complex remains unknown, our results support the hypothesis that UbiK is an accessory factor of Ubi enzymes and facilitates UQ biosynthesis by acting as an assembly factor, a targeting factor, or both.Agence Nationale de la Recherche ANR-15-CE11-0001-02Centre National de la Recherche Scientifique PICS07279French State Program "Investissements d'Avenir" ANR-11-LABX-001

Helping learned societies explore Plan S-compliant business models - A proposal

This unsuccessful grant proposal was submitted to the funding call 'Helping learned societies explore Plan S-compliant business models', from the Wellcome Trust in partnership with UK Research and Innovation (UKRI) and the Association of Learned & Professional Society Publishers (ALPSP). The funders sought 'to engage the services of a consultant to explore a range of potential strategies and business models through which learned societies could adapt and thrive under Plan S' (https://wellcome.ac.uk/sites/default/files/learned-societies-consultancy-request-for-proposals.pdf)

Early Quaternary sedimentary processes and palaeoenvironments in the central North Sea

A number of elongate trough-like features are observed in the early Quaternary succession of the central North Sea basin. A definitive model of formation for the features remains unclear but the troughs may aid in our understanding of the depositional environment of the early Quaternary. In total, 380 troughs were mapped over 11 000 km2 using continuous 3D seismic data and analysed in conjunction with well log data and understanding of the probable palaeogeographical context. The troughs were formed in a marine setting on the slope of a large clinoform set during a period of rapid progradation. The geometry and infill of the troughs, as well as the marine setting, strongly support a model of repeated density-driven downslope flows which excavate and then infill the troughs perpendicular to the strike of the slope. A subset of the troughs are observed to form parallel to the strike in such a way that cannot be easily explained by downslope processes alone. A number of possible models are considered for the formation of these along-slope troughs; here we conclude that the most likely scenario involves modification of the downslope flows by currents which divert the features along-slope while maintaining the erosive nature of the flow

Open Scholarship and the need for collective action

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Mid-Pleistocene thin-skinned glaciotectonic thrusting of the Aberdeen Ground Formation, Central Graben region, central North Sea

This paper presents the results of a high-resolution 2D seismic survey of mid-Pleistocene glaciogenic sediments in the Central Graben region of the central North Sea. Sediments have undergone major glaciotectonic thrusting and folding associated with the repeated southerly advance of a mid-Pleistocene ice sheet. The total observed length of the thrust-stacked section is approximately 5–6 km, comprising a series of discrete thrust slices, which range in length from  700 m. The basal detachment of the thrust complex occurs at a depth of ca. 220 m below the sea bed within the upper Aberdeen Ground Formation. A thin-skinned glaciotectonic model involving proglacial to ice-marginal glaciotectonic thrusting followed by post-tectonic deposition is proposed. Initial ice advance led to the over-pressurizing of groundwater within a laterally extensive sand sheet in the upper Aberdeen Ground Formation, promoting the formation of a major décollement surface at the base of the developing thrust-stack. Over-pressurization of the groundwater system is thought to have occurred in response to rapid ice advance, suggesting that the development of large-scale thrust complexes may be associated with surge-type behaviour. The proposed model evidences complex dynamics of mid-Pleistocene ice sheets within the central North Sea

The behaviour of repeat visitors to museums: Review and empirical findings

This study presents a theoretical and operational framework for analysing repeat visit to museums. Starting from the literature on repeat visit in tourism, the specificities of these cultural attractions are made explicit through a review of theoretical and applied works. Consistently with previous contributors, the paper suggests that the analysis of actual past behaviours has to be preferred to the one of attitudes. The application of proper econometric models is also remarked in order to put into account individual profiles. Information coming from three techniques is then used in an integrated way in order to provide a more comprehensive view of the phenomenon. Evidence from an ad hoc survey suggests the necessity to give a greater attention to perceived cultural value during the visit, promoting cultural events during the week and addressed to children, and taking care of those visitors that come from far places also through an integrated tourist supply. © 2013 Springer Science+Business Media Dordrecht

BRITICE Glacial Map, version 2: a map and GIS database of glacial landforms of the last British-Irish Ice Sheet

During the last glaciation, most of the British Isles and the surrounding continental shelf were covered by the British–Irish Ice Sheet (BIIS). An earlier compilation from the existing literature (BRITICE version 1) assembled the relevant glacial geomorphological evidence into a freely available GIS geodatabase and map (Clark et al. 2004: Boreas 33, 359). New high-resolution digital elevation models, of the land and seabed, have become available casting the glacial landform record of the British Isles in a new light and highlighting the shortcomings of the V.1 BRITICE compilation. Here we present a wholesale revision of the evidence, onshore and offshore, to produce BRITICE version 2, which now also includes Ireland. All published geomorphological evidence pertinent to the behaviour of the ice sheet is included, up to the census date of December 2015. The revised GIS database contains over 170 000 geospatially referenced and attributed elements – an eightfold increase in information from the previous version. The compiled data include: drumlins, ribbed moraine, crag-and-tails, mega-scale glacial lineations, glacially streamlined bedrock (grooves, roches moutonnées, whalebacks), glacial erratics, eskers, meltwater channels (subglacial, lateral, proglacial and tunnel valleys), moraines, trimlines, cirques, trough-mouth fans and evidence defining ice-dammed lakes. The increased volume of features necessitates different map/database products with varying levels of data generalization, namely: (i) an unfiltered GIS database containing all mapping; (ii) a filtered GIS database, resolving data conflicts and with edits to improve geo-locational accuracy (available as GIS data and PDF maps); and (iii) a cartographically generalized map to provide an overview of the distribution and types of features at the ice-sheet scale that can be printed at A0 paper size at a 1:1 250 000 scale. All GIS data, the maps (as PDFs) and a bibliography of all published sources are available for download from: https://www.sheffield.ac.uk/geography/staff/clark_chris/britice