It is now becoming more accepted that tau hyperphosphorylation and the development of neurofibrillary tangles is more likely to be a mediator of neurodegeneration in AD than Ab. It is interesting that synaptophysin mRNA levels were unaffected as Ab, particularly soluble oligomers of Ab, has been shown to decrease expression of synaptic markers, including synaptophysin. However, this finding is not consistent across all studies, indicating that decreased synaptophysin expression may not be a direct consequence of Ab expression and that other additional factors may be necessary. It is important to note that only gross neurodegeneration would have been observed by the quantification measures used in this study and that the use other neuronal and cell death markers may have provided a more specific indication of neurodegeneration. Western blot and immunohistochemical processing failed to detect significant Ab40 and Ab42 protein expression in transduced brain regions. We do not believe that this was due to the use of inefficient viral vectors because Ab42 was detected in tissues injected with rAAV2-C100V717F-GFP or rAAV2-Ab42-GFP using the more sensitive ELISA SAR131675 VEGFR/PDGFR inhibitor technique, thus proving that these vectors were capable of producing Ab. Furthermore, there was strong transduction of all bi-cistronic rAAV2 vectors in the hippocampus and cerebellum, as shown by high expression levels of transgene mRNA and post-IRES GFP protein, the latter produced only after C100 or Ab protein translation. Finally, injection of rAAV2-Ab40-GFP and rAAV2-Ab42-GFP resulted in the development of obvious brain pathology that was unique to each Ab isoform and was not present after injection of vehicle or rAAV2-GFP controls, strongly suggesting that the Ab produced as a result of rAAV2 vector injection was responsible for the observed pathologies. We hypothesise that the inability to detect Ab using the less sensitive immunohistochemistry and western blotting methods, and the observation of variance between animals in the amount of Ab detected using ELISA, was due to rapid clearance and/or Axitinib degradation of Ab.Ab levels are highly regulated in vivo by rapid clearance across the blood brain barrier, phagocytosis by glia and degradation by multiple enzymes. Enhancement of any of these mechanisms could result in low Ab levels. Indeed, some of the pathology observed in vivo including microgliosis and infiltration of cells from the periphery indicate that Ab degradation may have been increased in response to expression of Ab as both microglia and infiltrating monocytes are capable of Ab phagocytosis and enhance degradation. Increased Ab clearance may also explain the lack of Ab40 detected using the ELISA-mutiplex assay, as this isoform is more readily cleared and degraded than Ab42. Furthermore, the Indiana mutation promotes the preferential production of Ab42 rather than Ab40, therefore the presence of this mutation and the hypothesised increased clearance of Ab could account for the very low levels of Ab40 observed after injection of rAAV2-C100V717F-GFP. Lack of available tissue prevented ELISA-based quantification of Ab40 levels after injection of rAAV2-Ab40-GFP. An intriguing finding was that, while significant levels of Ab42 protein were detected in the cerebellum but not in the hippocampus, injection of rAAV2 vectors into the hippocampus resulted in greater pathological changes than those seen in the cerebellum.