Integrated Microarray-based Tools for Detection of Genomic DNA Damage and Repair Mechanisms.

The genetic information contained within the DNA molecule is highly susceptible to chemical and physical insult, caused by both endogenous and exogenous sources that can generate in the order of thousands of lesions a day in each of our cells (Lindahl, Nature 362(6422):709-715, 1993). DNA damages interfere with DNA metabolic processes such as transcription and replication and can be potent inhibitors of cell division and gene expression. To combat these regular threats to genome stability, a host of DNA repair mechanisms have evolved.

Global genome nucleotide excision repair is organized into domains that promote efficient DNA repair in chromatin.

The rates at which lesions are removed by DNA repair can vary widely throughout the genome, with important implications for genomic stability. To study this, we measured the distribution of nucleotide excision repair (NER) rates for UV-induced lesions throughout the budding yeast genome. By plotting these repair rates in relation to genes and their associated flanking sequences, we reveal that, in normal cells, genomic repair rates display a distinctive pattern, suggesting that DNA repair is highly organized within the genome.

Sandcastle: software for revealing latent information in multiple experimental ChIP-chip datasets via a novel normalisation procedure.

ChIP-chip is a microarray based technology for determining the genomic locations of chromatin bound factors of interest, such as proteins. Standard ChIP-chip analyses employ peak detection methodologies to generate lists of genomic binding sites. No previously published method exists to enable comparative analyses of enrichment levels derived from datasets examining different experimental conditions.

3D-DIP-Chip: a microarray-based method to measure genomic DNA damage.

Genotoxins cause DNA damage, which can result in genomic instability. The genetic changes induced have far-reaching consequences, often leading to diseases such as cancer. A wide range of genotoxins exists, including radiations and chemicals found naturally in the environment, and in man-made forms created by human activity across a variety of industries.

Site-specific management of nematodes pitfalls and practicalities.

The greatest constraint to potato production in the United Kingdom (UK) is damage by the potato cyst nematodes (PCN) Globodera pallida and G. rostochiensis. Management of PCN depends heavily on nematicides, which are costly.