Selective inhibitors of trypanosomal uridylyl transferase RET1 establish druggability of RNA post-transcriptional modifications.

Non-coding RNAs are crucial regulators for a vast array of cellular processes and have been implicated in human disease. These biological processes represent a hitherto untapped resource in our fight against disease. In this work we identify small molecule inhibitors of a non-coding RNA uridylylation pathway. The TUTase family of enzymes is important for modulating non-coding RNA pathways in both human cancer and pathogen systems. We demonstrate that this new class of drug target can be accessed with traditional drug discovery techniques. Using the Trypanosoma brucei TUTase, RET1, we identify TUTase inhibitors and lay the groundwork for the use of this new target class as a therapeutic opportunity for the under-served disease area of African Trypanosomiasis. In a broader sense this work demonstrates the therapeutic potential for targeting RNA post-transcriptional modifications with small molecules in human disease.This work was supported by two grants from the European Research Council (RG58558, RG67639) and a grant from Cancer Research UK (RG51661) to E.A.MThis is the author accepted manuscript. The final version is available from [publisher] via http://dx.doi.org/10.1080/15476286.2015.113742

Tolerance to extreme hot and cold temperatures in the EU-protected terrestrial slug Geomalacus maculosus

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Nematode associates and susceptibility of a protected slug (Geomalacus maculosus) to four biocontrol nematodes

The impact of selected entomopathogenic nematodes and Phasmarhabditis hermaphrodita on the European-Union-protected slug Geomalacus maculosus and the sympatric Lehmannia marginata was investigated. There was no significant difference in mortality between slugs treated with nematodes and their controls. The presence of P. hermaphrodita in two G. maculosus cadavers may be the result of necromenic behaviour. This study constitutes the first record of P. californica in Europe

Does Landscape Structure Affect the Presence of Woodland Specialist Pollinators in Farmland? Implications for Agri-Environment Scheme Design

Publication history: Accepted - 19 October 2021; Published - 16 March 2022.natural or semi-natural habitats to nest and/or forage. Landscape structure has been shown to influence pollinator communities and understanding how landscape structure affects farmland pollinators can improve Agri-Environment Schemes (AES). This study explored how landscape metrics affect the presence of pollinators associated with woody vegetation in farmland in the Republic of Ireland. Two study regions were selected, and pollinators were collected using pan traps placed in farm linear features. Hoverfly and bee species were selected based on their body size and association with woody vegetation. Relevant landscape structure metrics were extracted from around each trap and used to develop explanatory models for the abundance of pollinators. The total abundance of target species was relatively low but correlated with three explanatory variables: the connectivity of the linear feature to woodlands; the distance from the trap to the closest woodland; and edge density. Hoverfly and bee abundance data, when analysed separately, showed significant differences within regions. Results seem to indicate that incentivising the connectivity of farm linear features to surrounding woodland patches and increasing optimal habitat availability in agricultural landscapes could benefit woodland specialists. This information is helpful to improving AES design.This work was supported by the Irish Department of Agriculture, Food and the Marine (DAFM) (RSF15_S_619). Open Access funding provided by IReL

Aflatoxin-Induced TP53 R249S Mutation in HepatoCellular Carcinoma in Thailand: Association with Tumors Developing in the Absence of Liver Cirrhosis

Primary Liver Cancer (PLC) is the leading cause of death by cancer among males in Thailand and the 3rd among females. Most cases are hepatocellular carcinoma (HCC) but cholangiocarcinomas represent between 4 and 80% of liver cancers depending upon geographic area. Most HCC are associated with chronic infection by Hepatitis B Virus while a G→T mutation at codon 249 of the TP53 gene, R249S, specific for exposure to aflatoxin, is detected in tumors for up to 30% of cases. We have used Short Oligonucleotide Mass Analysis (SOMA) to quantify free circulating R249S-mutated DNA in plasma using blood specimens collected in a hospital case:control study. Plasma R249S-mutated DNA was detectable at low concentrations (≥67 copies/mL) in 53 to 64% of patients with primary liver cancer or chronic liver disease and in 19% of controls. 44% of patients with HCC and no evidence of cirrhosis had plasma concentrations of R249S-mutated DNA ≥150 copies/mL, compared to 21% in patients with both HCC and cirrhosis, 22% in patients with cholangiocarcinoma, 12% in patients with non-cancer chronic liver disease and 3% of subjects in the reference group. Thus, plasma concentrations of R249S-mutated DNA ≥150 copies/mL tended to be more common in patients with HCC developing without pre-existing cirrhosis (p = 0.027). Overall, these results support the preferential occurrence of R249S-mutated DNA in HCC developing in the absence of cirrhosis in a context of HBV chronic infection

Monitoring the EU protected Geomalacus maculosus (Kerry Slug): what are the factors affecting catch returns in open and forested habitats?

Geomalacus maculosus is a slug species protected under EU law with a distribution limited to the west of Ireland and north-west Iberia. The species, originally thought to be limited within Ireland to deciduous woodland and peatland, has been found in a number of commercial conifer plantations since 2010. While forest managers are now required to incorporate the protection of the species where it is present, no clear species monitoring protocols are currently available. This study examines the efficacy of De Sangosse refuge traps across three habitats frequently associated with commercial forest plantations in Ireland and compares them with hand searching, a commonly used method for slug monitoring. Catch data during different seasons and under different weather conditions are also presented. Results indicate that autumn is the optimal time for sampling G. maculosus but avoiding extremes of hot or cold weather. While refuge traps placed at 1.5 m on trees in mature conifer plantations and directly on exposed rock in blanket peatlands result in significantly greater catches, hand searching is the most successful approach for clear-fell areas. Hand searches in clear-fell preceded by rain are likely to result in greater numbers caught. The results of this study form, for the first time, the basis for G. maculosus monitoring guidelines for forestry managers. © 2016, The Ecological Society of Japa

FOXM1 binds directly to non-consensus sequences in the human genome.

BACKGROUND: The Forkhead (FKH) transcription factor FOXM1 is a key regulator of the cell cycle and is overexpressed in most types of cancer. FOXM1, similar to other FKH factors, binds to a canonical FKH motif in vitro. However, genome-wide mapping studies in different cell lines have shown a lack of enrichment of the FKH motif, suggesting an alternative mode of chromatin recruitment. We have investigated the role of direct versus indirect DNA binding in FOXM1 recruitment by performing ChIP-seq with wild-type and DNA binding deficient FOXM1. RESULTS: An in vitro fluorescence polarization assay identified point mutations in the DNA binding domain of FOXM1 that inhibit binding to a FKH consensus sequence. Cell lines expressing either wild-type or DNA binding deficient GFP-tagged FOXM1 were used for genome-wide mapping studies comparing the distribution of the DNA binding deficient protein to the wild-type. This shows that interaction of the FOXM1 DNA binding domain with target DNA is essential for recruitment. Moreover, analysis of the protein interactome of wild-type versus DNA binding deficient FOXM1 shows that the reduced recruitment is not due to inhibition of protein-protein interactions. CONCLUSIONS: A functional DNA binding domain is essential for FOXM1 chromatin recruitment. Even in FOXM1 mutants with almost complete loss of binding, the protein-protein interactions and pattern of phosphorylation are largely unaffected. These results strongly support a model whereby FOXM1 is specifically recruited to chromatin through co-factor interactions by binding directly to non-canonical DNA sequences.We would like to acknowledge the Genomics and bioinformatics core at the CRUK Research Institute for the Illumina sequencing and the Proteomics core for the LC/MS-MS protein analysis for the RIME experiments. We acknowledge the support from The University of Cambridge and Cancer Research UK. The Balasubramanian Laboratory is supported by core funding from Cancer Research UK (C14303/A17197). SB is a Wellcome Trust Principle Investigator.This is the final version of the article. It first appeared from BioMed Central via http://dx.doi.org/10.1186/s13059-015-0696-

Developing a predictive modelling capacity for a climate change-vulnerable blanket bog habitat: Assessing 1961-1990 baseline relationships

Aim: Understanding the spatial distribution of high priority habitats and developing predictive models using climate and environmental variables to replicate these distributions are desirable conservation goals. The aim of this study was to model and elucidate the contributions of climate and topography to the distribution of a priority blanket bog habitat in Ireland, and to examine how this might inform the development of a climate change predictive capacity for peat-lands in Ireland. Methods: Ten climatic and two topographic variables were recorded for grid cells with a spatial resolution of 1010 km, covering 87% of the mainland land surface of Ireland. Presence-absence data were matched to these variables and generalised linear models (GLMs) fitted to identify the main climatic and terrain predictor variables for occurrence of the habitat. Candidate predictor variables were screened for collinearity, and the accuracy of the final fitted GLM was evaluated using fourfold cross-validation based on the area under the curve (AUC) derived from a receiver operating characteristic (ROC) plot. The GLM predicted habitat occurrence probability maps were mapped against the actual distributions using GIS techniques. Results: Despite the apparent parsimony of the initial GLM using only climatic variables, further testing indicated collinearity among temperature and precipitation variables for example. Subsequent elimination of the collinear variables and inclusion of elevation data produced an excellent performance based on the AUC scores of the final GLM. Mean annual temperature and total mean annual precipitation in combination with elevation range were the most powerful explanatory variable group among those explored for the presence of blanket bog habitat. Main conclusions: The results confirm that this habitat distribution in general can be modelled well using the non-collinear climatic and terrain variables tested at the grid resolution used. Mapping the GLM-predicted distribution to the observed distribution produced useful results in replicating the projected occurrence of the habitat distribution over an extensive area. The methods developed will usefully inform future climate change predictive modelling for Irelan

Quantifying phenotype-environment matching in the protected kerry spotted slug (mollusca: gastropoda) using digital photography: exposure to uv radiation determines cryptic colour morphs

Background: Animal colours and patterns commonly play a role in reducing detection by predators, social signalling or increasing survival in response to some other environmental pressure. Different colour morphs can evolve within populations exposed to different levels of predation or environmental stress and in some cases can arise within the lifetime of an individual as the result of phenotypic plasticity. Skin pigmentation is variable for many terrestrial slugs (Mollusca: Gastropoda), both between and within species. The Kerry spotted slug Geomalacus maculosus Allman, an EU protected species, exhibits two distinct phenotypes: brown individuals occur in forested habitats whereas black animals live in open habitats such as blanket bog. Both colour forms are spotted and each type strongly resembles the substrate of their habitat, suggesting that G. maculosus possesses camouflage. Results: Analysis of digital images of wild slugs demonstrated that each colour morph is strongly and positively correlated with the colour properties of the background in each habitat but not with the substrate of the alternative habitats, suggesting habitat-specific crypsis. Experiments were undertaken on laboratory-reared juvenile slugs to investigate whether ultraviolet (UV) radiation or diet could induce colour change. Exposure to UV radiation induced the black (bog) phenotype whereas slugs reared in darkness did not change colour. Diet had no effect on juvenile colouration. Examination of skin tissue from specimens exposed to either UV or dark treatments demonstrated that UV-exposed slugs had significantly higher concentrations of black pigment in their epithelium. Conclusions: These results suggest that colour dimorphism in G. maculosus is an example of phenotypic plasticity which is explained by differential exposure to UV radiation. Each resulting colour morph provides incidental camouflage against the different coloured substrate of each habitat. This, to our knowledge, is the first documented example of colour change in response to UV radiation in a terrestrial mollusc. Pigmentation appears to be correlated with a number of behavioural traits in G. maculosus, and we suggest that understanding melanisation in other terrestrial molluscs may be useful in the study of pestiferous and invasive species. The implications of colour change for G. maculosus conservation are also discussed

Slugs: A Guide to the Invasive and Native Fauna of California

The first thorough key to the identification of slugs in California. You may think all slugs look alike, but on closer examination you will be surprised at how they differ. Color photographs