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

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

Towards whole genome association genetic scans in barley

In crop plants, the potential of association mapping, with the objective of estimating the position of genes conferring a specific trait or phenotype using linkage disequilibrium (LD) between alleles of genetically mapped markers, has recently become a focus of considerable interest. One major attraction of association genetics is the potential to locate genes responsible for a wide range of traits in a single sample population using pre-existing phenotypic data that has been collected during crop improvement and cultivar registration programs. This study testify to the potential of exploiting whole genome LD-scans to locate genes controlling key biological traits in cultivated barley. We are currently increasing the density of markers, particularly those with a MAF >0.1, by developing two further pilot OPAs, which in due course will be compressed into two commercially available platforms for high throughput low cost genotyping in cultivated barley. In the immediate future these will be used in large association genetic studies in the UK and US involving approximately 4000 barley genotypes with the aim of realising the potential for whole genome association genetic scans in cultivated barley

UK Geoenergy Observatories Glasgow: GGC01 cored, seismic monitoring borehole – final data release

This report provides an overview of information contained in the final data release for the UK Geoenergy Observatories Glasgow borehole GGC01. This final data release supersedes the initial and intermediate data releases (Starcher et al. 2019; Kearsey et al. 2019). It includes additional information on core scan data and core-wireline depth integration. The cored, seismic monitoring borehole GGC01 (BGS SOBI number NS66SW BJ 3754, BGS ID 20650619) was drilled between 19 November and 12 December 2018 producing a core of 102 mm diameter. The borehole was wireline logged in December 2018 and a string of 5 seismometers were installed in February 2019. The core was transported to the National Geological Repository (NGR) at BGS Keyworth and was curated into 1 m core boxes. State-of-the-art core scanners have been used to collect along core datasets. This final data release includes optical images (whole core and slabbed core), radiographic images, MSCL-S (geophysical), NIR and XRF (mineralogical and chemical) core scan data. Also included in this final release is the material from the previous releases including sedimentary, discontinuity and engineering logs, wireline/geophysical downhole logs, drillers’ logs and sample information

Functional diversity of marine ecosystems after the Late Permian mass extinction event

Article can be accessed from http://www.nature.com/ngeo/journal/v7/n3/full/ngeo2079.htmlThe Late Permian mass extinction event was the most severe such crisis of the past 500 million years and occurred during an episode of global warming. It is assumed to have had significant ecological impact, but its effects on marine ecosystem functioning are unknown and the patterns of marine recovery are debated. We analysed the fossil occurrences of all known Permian-Triassic benthic marine genera and assigned each to a functional group based on their inferred life habit. We show that despite the selective extinction of 62-74% of marine genera there was no significant loss of functional diversity at the global scale, and only one novel mode of life originated in the extinction aftermath. Early Triassic marine ecosystems were not as ecologically depauperate as widely assumed, which explains the absence of a Cambrian-style Triassic radiation in higher taxa. Functional diversity was, however, significantly reduced in particular regions and habitats, such as tropical reefs, and at these scales recovery varied spatially and temporally, probably driven by migration of surviving groups. Marine ecosystems did not return to their pre-extinction state, however, and radiation of previously subordinate groups such as motile, epifaunal grazers led to greater functional evenness by the Middle Triassic

UK Geoenergy Observatories Glasgow: GGC01 cored, seismic monitoring borehole – intermediate data release

This report gives an overview of information related to an intermediate data release of the borehole information pack for UK Geoenergy Observatories: Glasgow borehole GGC01. The cored, seismic monitoring borehole GGC01 (BGS SOBI number NS66SW BJ 3754, BGS ID 20650619) was drilled between 19 November and 12 December 2018 producing a core of 102 mm diameter. The borehole was wireline logged in December 2018 and a string of 5 seismometers were installed in February 2019. The core was transported to the National Geological Repository (NGR) at BGS Keyworth and was curated into 1 m core boxes. State-of-the-art core scanners are being used to collect radiographic, CT, optical images, geophysical log and XRF along core datasets. Optical images and radiographic images are included in the intermediate release. Also included are sedimentary, discontinuity and engineering log

‘Block and basin’ style rift basins: sedimentological insights from the Mississippian Fell Sandstone Formation

The block and basin tectonostratigraphic framework for the northern Pennine (rift) Basin, within which buoyant granite intrusions core intra-basin fault-bounded blocks, has long held traction. However, many of the elements of this framework are rooted in primitive tectonic models and, perhaps unsurprisingly, corresponding depositional models often reflect this. Using sedimentological and sedimentary provenance approaches, the synrift (Mississippian) fluvio-deltaic Fell Sandstone Formation and age-equivalent strata within the northern Pennine Basin are examined. Highlighted divergences from classically depicted models relate to occurrences of pre-Carboniferous basement domes or monoclines, which are unbounded by major vertically displacing (>100 m) fault systems. Such structures in the northern Pennine Basin are all granite-cored and their origins are associated with their buoyancy and flexural isostatic processes. One such basement dome, the Cheviot Block, confined and deflected the Fell Sandstone fluvio-deltaic system from the west, causing locally elevated net sand content and variations in the dominant palaeodrainage direction. Central parts of the Alston Block, which forms a regional monocline along an east–west axis, were comparatively uplifted because of flexural isostatic responses to granite intrusions. The findings presented are at variance not only with classically depicted depositional models for the region, but also with more general depictions of dominantly normal fault-driven rift basin systems

Diagnosis of oesophageal cancer by detection of minichromosome maintenance 5 protein in gastric aspirates

Symptomatic oesophageal cancer is usually advanced and the prognosis poor. Lethality of symptomatic oesophageal cancer has motivated screening for these diseases earlier in their evolution, but reliable methods for early diagnosis remain elusive. We have demonstrated that dysregulated expression of minichromosome maintenance (MCM) proteins 2–7 is characteristic of early epithelial carcinogenesis, and that these key DNA replication initiation factors can be used as diagnostic markers for cervical and genito-urinary tract cancer. In this study, we investigated whether minichromosome maintenance protein 5 (Mcm5) can be used to detect oesophageal cancer cells in gastric aspirates. Two monoclonal antibodies raised against His-tagged human Mcm5 were used in a time-resolved immunofluorometric assay to measure Mcm5 levels in cells isolated from gastric aspirates of 40 patients undergoing gastroscopy for suspected or known oesophageal carcinoma or symptoms of dyspepsia. The test discriminated with high specificity and sensitivity between patients with and without oesophageal cancer (85% sensitivity (95% confidence interval (CI)=62–97%), 85% specificity (CI=66–96%)), as demonstrated by the large area under the receiver operating characteristics curve (0.93 (95% CI=0.85–0.99)). Elevated levels of Mcm5 in gastric aspirates are highly predictive of oesophageal cancer. This simple test for oesophageal cancer is readily automated with potential applications in primary diagnosis, surveillance and screening

Robust Detection and Genotyping of Single Feature Polymorphisms from Gene Expression Data

It is well known that Affymetrix microarrays are widely used to predict genome-wide gene expression and genome-wide genetic polymorphisms from RNA and genomic DNA hybridization experiments, respectively. It has recently been proposed to integrate the two predictions by use of RNA microarray data only. Although the ability to detect single feature polymorphisms (SFPs) from RNA microarray data has many practical implications for genome study in both sequenced and unsequenced species, it raises enormous challenges for statistical modelling and analysis of microarray gene expression data for this objective. Several methods are proposed to predict SFPs from the gene expression profile. However, their performance is highly vulnerable to differential expression of genes. The SFPs thus predicted are eventually a reflection of differentially expressed genes rather than genuine sequence polymorphisms. To address the problem, we developed a novel statistical method to separate the binding affinity between a transcript and its targeting probe and the parameter measuring transcript abundance from perfect-match hybridization values of Affymetrix gene expression data. We implemented a Bayesian approach to detect SFPs and to genotype a segregating population at the detected SFPs. Based on analysis of three Affymetrix microarray datasets, we demonstrated that the present method confers a significantly improved robustness and accuracy in detecting the SFPs that carry genuine sequence polymorphisms when compared to its rivals in the literature. The method developed in this paper will provide experimental genomicists with advanced analytical tools for appropriate and efficient analysis of their microarray experiments and biostatisticians with insightful interpretation of Affymetrix microarray data