Towards whole genome as s ociation genetic s cans in barley

Mapping traits and isolating the underlying genes is largely based on following the inheritance of both the trait and molecular markers in experimental populations from crosses between parents that contrast for the trait under study

Real-time imaging of DNA damage in yeast cells using ultra-short near-infrared pulsed laser irradiation

Analysis of accumulation of repair and checkpoint proteins at repair sites in yeast nuclei has conventionally used chemical agents, ionizing radiation or induction of endonucleases to inflict localized damage. In addition to these methods, similar studies in mammalian cells have used laser irradiation, which has the advantage that damage is inflicted at a specific nuclear region and at a precise time, and this allows accurate kinetic analysis of protein accumulation at DNA damage sites. We show here that it is feasible to use short pulses of near-infrared laser irradiation to inflict DNA damage in subnuclear regions of yeast nuclei by multiphoton absorption. In conjunction with use of fluorescently-tagged proteins, this allows quantitative analysis of protein accumulation at damage sites within seconds of damage induction. PCNA accumulated at damage sites rapidly, such that maximum accumulation was seen approximately 50 s after damage, then levels declined linearly over 200-1000 s after irradiation. RPA accumulated with slower kinetics such that hardly any accumulation was detected within 60 s of irradiation, and levels subsequently increased linearly over the next 900 s, after which levels were approximately constant (up to ca. 2700 s) at the damage site. This approach complements existing methodologies to allow analysis of key damage sensors and chromatin modification changes occurring within seconds of damage inception

Reduced Dwell-Fatigue Resistance in a Ni-Base Superalloy After Short-Term Thermal Exposure

The effect of short-term thermal exposure on microstructure and dwell-fatigue resistance of Ni-base superalloy 718Plus was investigated. Contrary to previous studies performed after long-term exposure, an increase in the dwell-fatigue crack growth rate was observed, which was connected to a small increase in the size of the hardening precipitates. The proposed controlling mechanism was the stress relaxation rate at the crack tip, and based on this a schematic model for the development of the properties during exposure is presented

Competitive aminal formation during the synthesis of a highly soluble, isopropyl-decorated imine porous organic cage

The synthesis of a new porous organic cage decorated with isopropyl moieties (CC21) was achieved from the reaction of triformylbenzene and an isopropyl functionalised diamine. Unlike structurally analogous porous organic cages, its synthesis proved challenging due to competitive aminal formation, rationalised using control experiments and computational modelling. The use of an additional amine was found to increase conversion to the desired cage

UKGEOS: Glasgow Geothermal Energy Research Field Site (GGERFS): initial summary of the geological platform

The preferred second UKGEOS site is at Clyde Gateway, in the east end of Glasgow, Scotland. The focus of this, the Glasgow Geothermal Energy Research Field Site (GGERFS), is on characterising and monitoring the subsurface for minewater and hot sedimentary aquifer geothermal energy, and for cooling and heat storage. This report details BGS data and knowledge at late 2016, to define initial characterisation of the ‘geological platform’ relevant for the planning of a geothermal research facility and associated environmental baseline monitoring. The report covers knowledge of the bedrock and superficial deposits geology, abandoned coal mines, hydrogeology, geothermal datasets, geochemistry, remote sensed data, seismicity, stress fields, engineering geology and rock property datasets. BGS holds a great deal of legacy borehole, mining and geochemistry data and has updated existing bedrock and superficial deposits models of the area. However, deep borehole and seismic data are lacking to define the geology and structure of the area below a few hundred metres. Hydrogeological and temperature data are also lacking for the bedrock strata. Regional datasets and knowledge have (and can be further) used to reduce uncertainty and risk in these aspects of the geological characterisation

Mucosal antibodies to the C terminus of toxin A prevent colonization of Clostridium difficile

Mucosal immunity is considered important for protection against Clostridium difficile infection (CDI). We show that in hamsters immunized with Bacillus subtilis spores expressing a carboxy-terminal segment (TcdA26-39) of C. difficile toxin A, no colonization occurs in protected animals when challenged with C. difficile strain 630. In contrast, animals immunized with toxoids showed no protection and remained fully colonized. Along with neutralizing toxins, antibodies to TcdA26-39 (but not to toxoids), whether raised to the recombinant protein or to TcdA26-39 expressed on the B. subtilis spore surface, cross-react with a number of seemingly unrelated proteins expressed on the vegetative cell surface or spore coat of C. difficile. These include two dehydrogenases, AdhE1 and LdhA, as well as the CdeC protein that is present on the spore. Anti-TcdA26-39 mucosal antibodies obtained following immunization with recombinant B. subtilis spores were able to reduce the adhesion of C. difficile to mucus-producing intestinal cells. This cross-reaction is intriguing yet important since it illustrates the importance of mucosal immunity for complete protection against CDI

Quantification of DNA-associated proteins inside eukaryotic cells using single-molecule localization microscopy

Development of single-molecule localization microscopy techniques has allowed nanometre scale localization accuracy inside cells, permitting the resolution of ultra-fine cell structure and the elucidation of crucial molecular mechanisms. Application of these methodologies to understanding processes underlying DNA replication and repair has been limited to defined in vitro biochemical analysis and prokaryotic cells. In order to expand these techniques to eukaryotic systems, we have further developed a photo-activated localization microscopy-based method to directly visualize DNA-associated proteins in unfixed eukaryotic cells. We demonstrate that motion blurring of fluorescence due to protein diffusivity can be used to selectively image the DNA-bound population of proteins. We designed and tested a simple methodology and show that it can be used to detect changes in DNA binding of a replicative helicase subunit, Mcm4, and the replication sliding clamp, PCNA, between different stages of the cell cycle and between distinct genetic backgrounds

Urban geoscience report : the value of geoscience data, information and knowledge for transport and linear infrastructure projects

New transport and urban infrastructure provision lies at the centre of UK government’s Build Back Better campaign and the Levelling-Up Agenda, to deliver significant socio-economic value to local economies, through provision of jobs and supply contracts, and enhancing well-being through greater local access to services. This will comprise large scale investment in major infrastructure and construction projects like HS2, Crossrail, and major flood risk management programmes as well as the provision of housing and the rapid deployment of fibre and 5G. To maximise the value of investment in new infrastructure the UK Government has set targets for improved productivity, efficiency, and adoption of environment-sensitive principles in the construction sector with the introduction of ‘Project Speed’ and the ‘Faster, Better, Greener’ approach. A number of recent initiatives have highlighted the value of subsurface data sharing to support construction and infrastructure development, and wider subsurface management. These include the Geospatial Commission’s National Underground Asset Register; Dig-to-Share -an Infrastructure Industry Innovation Partnership project; Project Iceberg; and the EU Sub-Urban COST Action. These initiatives have been successful in bringing together public and private sector bodies to demonstrate the potential benefits arising from the deposition and (re-)use of geoscience data and information. Despite these successes the value of geological and geotechnical data throughout the infrastructure and construction lifecycle is still under appreciated, resulting in inefficiency and reduced productivity. It has been estimated that unforeseen ground conditions contribute to significant delays in 20-60% of transport and linear infrastructure developments, and budget overruns, typically over 10%, are recorded across the industry. This report describes how geological data and knowledge is key to overcoming challenges associated with ground conditions and improving efficiency within planning and construction. Whilst the review is targeted to the transport and linear infrastructure sector, the observations on Ground Investigation (GI) data and geological data and support services are relevant to the broader construction lifecycle. Some of the wider social, economic and environmental benefits delivered when good GI and data management principles are applied are also highlighted. The report identifies the key datasets and services available from the BGS for those undertaking GI for new transport and linear infrastructure projects but more widely for those employed in construction and asset management. A number of cases studies are described which demonstrate the value of geological and geotechnical information for transport infrastructure, such as the Lower Thames Crossing, and Farringdon Station (CrossRail)

Anatomy, Age and Origin of an Intramontane Top Basin Surface (Sorbas Basin, Betic Cordillera, SE Spain)

Collisional mountain belts commonly develop intramontane basins from mechanical and isostatic subsidence during orogenic development. These frequently display a relict top surface, evidencing a change interval from basin infilling to erosion often via capture or overspill. Such surfaces provide markers that inform on orogenic growth patterns via climate and base level interplay. Here, we describe the top surface from the Sorbas Basin, a key intramontane basin within the Betic Cordillera (SE Spain). The surface is fragmentary comprising high elevation hilltops and discontinuous ridges developed onto the variably deformed final basin infill outcrop (Gochar Formation). We reconstruct surface configuration using DEM interpolation and apply 10Be/26Al cosmonuclides to assess surface formation timing. The surface is a degraded Early Pleistocene erosional pediment developed via autogenic switching of alluvial fan streams under stable dryland climate and base level conditions. Base-level lowering since the Middle Pleistocene focused headwards incision up interfan drainages, culminating in fan head capture and fan morphological preservation within the abandoned surface. Post abandonment erosion has lowered the basin surface by 31 m (average) and removed ~5.95 km3 of fill. Regional basin comparisons reveal a phase of Early Pleistocene surface formation, marking landscape stability following the most recent Pliocene-Early Pleistocene mountain building. Post-surface erosion rate quantification is low and in accordance with 10Be denudation rates typical of the low uplift Betic Cordillera.</jats:p

Palaeozoic petroleum systems of the Orcadian Basin to Forth Approaches, Quadrants 6 - 21, UK

This report synthesises the results of the 21CXRM Palaeozoic project to describe the Carboniferous and Devonian petroleum systems of the Orcadian Basin to Forth Approaches area (Quadrants 6 – 21). Petroleum systems of the Orcadian study area that involve significant Palaeozoic elements are not wholly contained within Devonian, Carboniferous and Permian strata. A number of producing fields attest to two main proven petroleum systems; i. Co-sourced Devonian oil (with Jurassic oil) within a Jurassic reservoir: the Beatrice, Jacky and Lybster fields; ii. Jurassic-sourced oil in a Devonian and/or Carboniferous reservoir: the Buchan, Stirling, Claymore, Highlander fields. (Jurassic-sourced oil in a Permian (Zechstein) reservoir is also proven in the Carnoustie, Ettrick and Claymore fields, and in a Rotliegend reservoir in the Dee discovery). A number of additional unproven petroleum system elements are considered in this report; i. Possibilities for Devonian and Carboniferous sourcing or co-sourcing (with Jurassic oil) of Devonian, Carboniferous and Permian (Rotliegend) reservoirs in those areas underlain by proven Palaeozoic source rock; ii. Possibilities for migrated Jurassic and/or Devonian and/or Carboniferous hydrocarbons onto horst blocks and the regional Grampian High, into basement, Palaeozoic or younger reservoirs. Focusing on frontier areas north and east of the Inner Moray Firth and from the north-eastern Forth Approaches to Grampian High, integration of a large volume of seismic, well, geophysical, organic geochemistry, maturity and reservoir property data at regional scale has established: Source rocks A wide extent of potential Devonian lacustrine source rocks mapped seismically from the Inner Moray Firth to the East Orkney Basin and north of the Halibut Horst. Geochemically-typed Devonian-sourced oil shows, oil seep data outside the area of mature Kimmeridge Clay Formation, burial depth and a limited organic geochemistry/maturity dataset indicative of Devonian source rocks that are potentially mature for oil generation outside the Inner Moray Firth. Good quality gas- and oil-prone Carboniferous source rocks are mapped from the Witch Ground Graben to north eastern end of the Forth Approaches. Wells drilled on highs indicate oil-window thermal maturity levels. Oil and gas shows and basin modelling indicate Carboniferous strata buried more deeply in adjacent basins may reach gas maturity levels, with Cenozoic maturation. Key source rock intervals are: o Lower Devonian, lacustrine Struie Formation (Quadrants 11, 12), oil prone. o Middle Devonian, lacustine Orcadia Formation and Eday Group (Quadrants 11- 15 and possibly Quadrants 19, 20), oil prone. o Visean – Namurian (lower-mid Carboniferous) fluvio-deltaic Firth Coal Formation, gas and oil prone. (This unit is age-equivalent of the Scremerston and Yoredale Formations, Cleveland Group source rocks in Quadrants 25-44