Evaluation of Non-destructive Molecular Diagnostics for the Detection of Neoparamoeba perurans

Peer reviewed paper. Citation: Downes, J. K., Rigby, M. L., Taylor, R. S., Maynard, B. T., MacCarthy, E., O’Connor, I., Marcos-Lopez M., Rodger H. D., Collins E., Ruane N. M. & Cook, M. T. (2017). Evaluation of Non-destructive Molecular Diagnostics for the Detection of Neoparamoeba perurans. Frontiers in Marine Science, 4. https://doi.org/10.3389/fmars.2017.00061 Link: https://www.frontiersin.org/articles/10.3389/fmars.2017.00061/full DOI: https://doi.org/10.3389/fmars.2017.00061 Cited as per the open access policy of Frontiers Media SA.Amoebic gill disease (AGD) caused by Neoparamoeba perurans, has emerged in Europe as a significant problem for the Atlantic salmon farming industry. Gross gill score is the most widely used and practical method for determining AGD severity on farms and informing management decisions on disease mitigation strategies. As molecular diagnosis of AGD remains a high priority for much of the international salmon farming industry, there is a need to evaluate the suitability of currently available molecular assays in conjunction with the most appropriate non-destructive sampling methodology. The aims of this study were to assess a non-destructive sampling methodology (gill swabs) and to compare a range of currently available real-time polymerase chain-reaction (PCR) assays for the detection of N. perurans. Furthermore a comparison of the non-destructive molecular diagnostics with traditional screening methods of gill scoring and histopathology was also undertaken. The study found that all molecular protocols assessed performed well in cases of clinical AGD with high gill scores. A TaqMan based assay (protocol 1) was the optimal assay based on a range of parameters including % positive samples from a field trial performed on fish with gill scores ranging from 0 to 5. A higher proportion of gill swab samples tested positive by all protocols than gill filament biopsies and there was a strong correlation between gill swabs tested by protocol 1 and gross gill score and histology scores. Screening for N. perurans using protocol 1 in conjunction with non-destructive gill swab samples was shown to give the best results

Nuclease dead Cas9 is a programmable roadblock for DNA replication

Limited experimental tools are available to study the consequences of collisions between DNA-bound molecular machines. Here, we repurpose a catalytically inactivated Cas9 (dCas9) construct as a generic, novel, targetable protein-DNA roadblock for studying mechanisms underlying enzymatic activities on DNA substrates in vitro. We illustrate the broad utility of this tool by demonstrating replication fork arrest by the specifically bound dCas9-guideRNA complex to arrest viral, bacterial and eukaryotic replication forks in vitro

Automatic Language-Independent Induction of Gazetteer Lists

Adaptation of existing Information Extraction (IE) systems to new languages and domains is the focus of much current research, but progress is often hindered by the lack of available resources to enable developers to get a new system up and running fast. It has previously been shown that a good set of gazetteer lists can have a vital role here, but creation of lists for a new language or domain can be time-consuming and laborious. In this paper we demonstrate a tool for inducing gazetteer lists from a small set of annotated corpora and creating a baseline IE system. We also describe an extension to this, using bootstrapping techniques in order to generate much larger volumes of noisy training texts. High quality results have been achieved in this way on Hindi, Chinese and Arabic