A study of various environmental factors on the growth, encystment and survival of free living amoebae : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Microbiology at Massey University

Free-living amoebae (FLA) are soil organisms which have a worldwide distribution. Interest was raised when they were implicated in two fatal and several non-fatal infections in humans. This investigation involved examination of the role and/or effect of several environmental factors on growth, encystment and cyst survival of FLA. The effect of K+, Na+ , Mg+2, Ca+2 and Fe+2/+3 on the growth of four species of amoebae (Naegleria gruberi, Naegleria fowleri, Acanthamoeba culbertsoni and Acanthamoeba castellanii) was investigated. Inhibition of growth rate increased as the cation concentration was increased. The roles of Mg+2 and Ca+2 in encystment were investigated and it was found that rather than being necessary, they were inhibitory. The survival of cysts under low temperatures and high cation concentrations was studied. Acanthamoeba proved to be resistant to adverse conditions once encysted. Naegleria were not affected by high cation levels but were adversely affected by low temperatures. A preliminary identification of two isolates from Ngawha Springs hot pools was undertaken showing both amoebae to be temperature tolerant Naegleria species

A Genomics-Based Classification of Human Lung Tumors

We characterized genome alterations in 1255 clinically annotated lung tumors of all histological subgroups to identify genetically defined and clinically relevant subtypes. More than 55% of all cases had at least one oncogenic genome alteration potentially amenable to specific therapeutic intervention, including several personalized treatment approaches that are already in clinical evaluation. Marked differences in the pattern of genomic alterations existed between and within histological subtypes, thus challenging the original histomorphological diagnosis. Immunohistochemical studies confirmed many of these reassigned subtypes. The reassignment eliminated almost all cases of large cell carcinomas, some of which had therapeutically relevant alterations. Prospective testing of our genomics-based diagnostic algorithm in 5145 lung cancer patients enabled a genome-based diagnosis in 3863 (75%) patients, confirmed the feasibility of rational reassignments of large cell lung cancer, and led to improvement in overall survival in patients with EGFR-mutant or ALK-rearranged cancers. Thus, our findings provide support for broad implementation of genome-based diagnosis of lung cancer