DNAReplication: a database of information and resources for the eukaryotic DNA replication community

DNAReplication (at http://www.dnareplication.net) has been set up as a freely available single resource to facilitate access to information on eukaryotic DNA replication. This database summarizes organism-sorted data on replication proteins in the categories of nomenclature, biochemical properties, motifs, interactions, modifications, structure, cell localization and expression, and general comments. Replication concepts are defined and a general model of the steps in DNA replication is presented. Links to relevant websites and homepages of replication labs are provided. The site also has an interactive section where links to recent replication papers are posted and readers are provided with the facility to post comments about each paper. The interactive and links pages are modified weekly and the whole site is updated annually

A minimally invasive immunocytochemical approach to early detection of oral squamous cell carcinoma and dysplasia

Squamous dysplasia of the oral cavity indicates increased risk of progression to squamous cell carcinoma (SCC). An important advance would be the development of a minimally invasive assay for identification of oral SCC and dysplasia. We have investigated the suitability in this context of immunostaining oral smears for minichromosome maintainance proteins (MCMs), sensitive and specific biomarkers of cell cycle entry. Immunohistochemical examination of 66 oral tissue samples showed a greater frequency of Mcm-2 expression in surface layers of moderate/severe dysplasia and SCC compared to benign keratosis/mild dysplasia. Immunocytochemistry for Mcm-2/Mcm-5 was performed on 101 oral smears. Conventional smears included 23 from normal mucosa, benign proliferative disease and mild dysplasia, all of which were MCM negative. Of 52 conventional smears of SCC tissue samples, 18 were inadequate. However, MCM-positive cells were present in 33/34 adequate samples. Of 26 liquid-based cytology smears, 19 out of 20 smears from SCC were adequate and all were MCM positive. Six smears from benign lesions were adequate and MCM negative. We conclude that MCMs are promising markers for early detection of oral SCC and dysplasia, particularly in a liquid-based cytology platform. Detection of MCMs would be amenable to automation and potentially applicable in the developing world. Further studies are now warranted

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

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

Expression of the cancer-associated DNA polymerase ε P286R in fission yeast leads to translesion synthesis polymerase dependent hypermutation and defective DNA replication.

Somatic and germline mutations in the proofreading domain of the replicative DNA polymerase ε (POLE-exonuclease domain mutations, POLE-EDMs) are frequently found in colorectal and endometrial cancers and, occasionally, in other tumours. POLE-associated cancers typically display hypermutation, and a unique mutational signature, with a predominance of C > A transversions in the context TCT and C > T transitions in the context TCG. To understand better the contribution of hypermutagenesis to tumour development, we have modelled the most recurrent POLE-EDM (POLE-P286R) in Schizosaccharomyces pombe. Whole-genome sequencing analysis revealed that the corresponding pol2-P287R allele also has a strong mutator effect in vivo, with a high frequency of base substitutions and relatively few indel mutations. The mutations are equally distributed across different genomic regions, but in the immediate vicinity there is an asymmetry in AT frequency. The most abundant base-pair changes are TCT > TAT transversions and, in contrast to human mutations, TCG > TTG transitions are not elevated, likely due to the absence of cytosine methylation in fission yeast. The pol2-P287R variant has an increased sensitivity to elevated dNTP levels and DNA damaging agents, and shows reduced viability on depletion of the Pfh1 helicase. In addition, S phase is aberrant and RPA foci are elevated, suggestive of ssDNA or DNA damage, and the pol2-P287R mutation is synthetically lethal with rad3 inactivation, indicative of checkpoint activation. Significantly, deletion of genes encoding some translesion synthesis polymerases, most notably Pol κ, partially suppresses pol2-P287R hypermutation, indicating that polymerase switching contributes to this phenotype

Drilling into mines for heat: geological synthesis of the UK Geoenergy Observatory in Glasgow and implications for mine water heat resources

Thermal energy from groundwater in abandoned, flooded, coal mines has the potential to make a significant contribution to decarbonisation of heat and Net-Zero carbon emissions. In Glasgow, UK, a subsurface observatory has been constructed for mine water heat and heat storage research. We synthesise geological and mine water resource findings from a four-year period of borehole planning, drilling, logging and testing. The heterogenous bedrock is typical of the Scottish Coal Measures Group, whereas superficial deposits are more sand- and gravel-dominated than prognosed. Mine water boreholes encountered workings in the Glasgow Upper, Glasgow Ell and Glasgow Main coal seams, proving water-filled voids, mine waste, fractured rock mass and intact coal pillars with high yields on initial hydrogeological testing. Whilst the depth and extent of mine workings delineated on mine abandonment plans proved accurate, metre-scale variability was expected and proved in the boreholes. A mine water reservoir classification established from the observatory boreholes highlights the resource potential in areas of total extraction, stowage, and stoop and room workings. Since their spatial extent is more extensive across the UK than shafts or roadways, increasing the mine water energy evidence base and reducing exploration risk in these types of legacy workings is important

Vgl1, a multi-KH domain protein, is a novel component of the fission yeast stress granules required for cell survival under thermal stress

Multiple KH-domain proteins, collectively known as vigilins, are evolutionarily highly conserved proteins that are present in eukaryotic organisms from yeast to metazoa. Proposed roles for vigilins include chromosome segregation, messenger RNA (mRNA) metabolism, translation and tRNA transport. As a step toward understanding its biological function, we have identified the fission yeast vigilin, designated Vgl1, and have investigated its role in cellular response to environmental stress. Unlike its counterpart in Saccharomyces cerevisiae, we found no indication that Vgl1 is required for the maintenance of cell ploidy in Schizosaccharomyces pombe. Instead, Vgl1 is required for cell survival under thermal stress, and vgl1Δ mutants lose their viability more rapidly than wild-type cells when incubated at high temperature. As for Scp160 in S. cerevisiae, Vgl1 bound polysomes accumulated at endoplasmic reticulum (ER) but in a microtubule-independent manner. Under thermal stress, Vgl1 is rapidly relocalized from the ER to cytoplasmic foci that are distinct from P-bodies but contain stress granule markers such as poly(A)-binding protein and components of the translation initiation factor eIF3. Together, these observations demonstrated in S. pombe the presence of RNA granules with similar composition as mammalian stress granules and identified Vgl1 as a novel component that required for cell survival under thermal stress

Overview of the 21CXRM Palaeozoic Project : a regional petroleum systems analysis of the offshore Carboniferous and Devonian of the UKCS

This report gives an overview of the 21CXRM Palaeozoic Project background, scope and products (Sections 1-3). It explains how the component reports and datasets of the project fit together. Overview technical information (e.g. key diagrams and charts applicable across the reports for each area) is reproduced in Sections 6 and 7 for reference, particularly as background for users of the specialist reports. A visual representation of the regional coverage and quantity of digital Palaeozoic Project products is given in Figure 1

Cdt1 proteolysis is promoted by dual PIP degrons and is modulated by PCNA ubiquitylation

Cdt1 plays a critical role in DNA replication regulation by controlling licensing. In Metazoa, Cdt1 is regulated by CRL4Cdt2-mediated ubiquitylation, which is triggered by DNA binding of proliferating cell nuclear antigen (PCNA). We show here that fission yeast Cdt1 interacts with PCNA in vivo and that DNA loading of PCNA is needed for Cdt1 proteolysis after DNA damage and in S phase. Activation of this pathway by ultraviolet (UV)-induced DNA damage requires upstream involvement of nucleotide excision repair or UVDE repair enzymes. Unexpectedly, two non-canonical PCNA-interacting peptide (PIP) motifs, which both have basic residues downstream, function redundantly in Cdt1 proteolysis. Finally, we show that poly-ubiquitylation of PCNA, which occurs after DNA damage, reduces Cdt1 proteolysis. This provides a mechanism for fine-tuning the activity of the CRL4Cdt2 pathway towards Cdt1, allowing Cdt1 proteolysis to be more efficient in S phase than after DNA damage

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