Browsing by Author "Deakin, Greg"
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Item Open Access The functional role of methylated short tandem repeats in early mouse development(Cranfield University, 2011-08) Deakin, Greg; Bessant, ConradShort tandem repeats, or microsatellites are ubiquitous throughout all genomes that have been explored. In common with other sequences, the DNA in microsatellites has DNA marks in the form of chromatin methylation. Regulation of DNA methylation and changes in their pattern is critical for the establishment of unique cell states throughout development in mammals. DNA methylation is extensively reprogrammed during the early phases of mammalian development to establish unique developmental patterning. Whether microsatellites are also reprogrammed with developmental patterns is unknown. In this thesis, we assessed the characteristics of di- and trinucleotide microsatellites in the NCBIM37 Mus musculus assembly and observed a marked difference in quantity and length of microsatellites of differing motif, not explained by any known mechanism. Secondly we assessed the quantities of di-, tri- and tetranucleotide microsatellites in experimentally determined methylomes of Mus musculus at various stages in development. Our results indicate that at least one tetranucleotide microsatellite motif and more tentatively a second trinucleotide microsatellite follow a pattern of methylation consistent with reprogramming. Finally we show that the genes containing these specific microsatellites in the NCBIM37 genome have strong links to known developmental processes.Item Open Access Investigating the inoculum dynamics of Cladosporium on the surface of raspberry fruits and in the air(Wiley, 2024-03-21) Farwell, Lauren Helen; Papp-Rupar, Matevz; Deakin, Greg; Magan, Naresh; Xu, XiangmingRaspberry production is under threat from the emerging fungal pathogenic genus Cladosporium. We used amplicon-sequencing, coupled with qPCR, to investigate how fruit age, fruit location within a polytunnel, polytunnel location and sampling date affected the fruit epiphytic microbiome. Fruit age was the most important factor impacting the fungal microbiome, followed by sampling date and polytunnel location. In contrast, polytunnel location and fruit age were important factors impacting the bacterial microbiome composition, followed by the sampling date. The within-tunnel location had a small significant effect on the fungal microbiome and no effect on the bacterial microbiome. As fruit ripened, fungal diversity increased and the bacterial diversity decreased. Cladosporium was the most abundant fungus of the fruit epiphytic microbiome, accounting for nearly 44% of all fungal sequences. Rotorod air samplers were used to study how the concentration of airborne Cladosporium inoculum (quantified by qPCR) varied between location (inside and outside the polytunnel) and time (daytime vs. nighttime). Quantified Cladosporium DNA was significantly higher during the day than the night and inside the polytunnel than the outside. This study demonstrated the dynamic nature of epiphytic raspberry fruit microbiomes and airborne Cladosporium inoculum within polytunnels, which will impact disease risks on raspberry fruit.